data_2AGN # _entry.id 2AGN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2AGN pdb_00002agn 10.2210/pdb2agn/pdb RCSB RCSB033870 ? ? WWPDB D_1000033870 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-07-25 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2013-12-18 5 'Structure model' 1 4 2019-12-18 6 'Structure model' 1 5 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Structure summary' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Source and taxonomy' 7 6 'Structure model' 'Data collection' 8 6 'Structure model' 'Database references' 9 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' database_2 2 5 'Structure model' em_image_scans 3 5 'Structure model' em_software 4 5 'Structure model' pdbx_entity_src_syn 5 6 'Structure model' chem_comp_atom 6 6 'Structure model' chem_comp_bond 7 6 'Structure model' database_2 8 6 'Structure model' em_3d_fitting_list 9 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_em_software.image_processing_id' 2 6 'Structure model' '_database_2.pdbx_DOI' 3 6 'Structure model' '_database_2.pdbx_database_accession' 4 6 'Structure model' '_em_3d_fitting_list.accession_code' 5 6 'Structure model' '_em_3d_fitting_list.initial_refinement_model_id' 6 6 'Structure model' '_em_3d_fitting_list.source_name' 7 6 'Structure model' '_em_3d_fitting_list.type' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2AGN _pdbx_database_status.recvd_initial_deposition_date 2005-07-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.db_id EMD-1138 _pdbx_database_related.details . _pdbx_database_related.content_type 'associated EM volume' # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Boehringer, D.' 1 'Thermann, R.' 2 'Ostareck-Lederer, A.' 3 'Lewis, J.D.' 4 'Stark, H.' 5 # _citation.id primary _citation.title 'Structure of the hepatitis C Virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES' _citation.journal_abbrev Structure _citation.journal_volume 13 _citation.page_first 1695 _citation.page_last 1706 _citation.year 2005 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16271893 _citation.pdbx_database_id_DOI 10.1016/j.str.2005.08.008 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Boehringer, D.' 1 ? primary 'Thermann, R.' 2 ? primary 'Ostareck-Lederer, A.' 3 ? primary 'Lewis, J.D.' 4 ? primary 'Stark, H.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'HCV-1B IRES RNA SUB-DOMAIN IIID' 9450.667 1 ? ? ? ? 2 polymer syn 'HCV IRES SUB-DOMAIN IIIB' 9595.754 1 ? ? ? ? 3 polymer syn 'HCV IRES DOMAIN II' 24776.691 1 ? ? ? ? 4 polymer syn '6 nt A-RNA helix' 4547.780 1 ? ? ? ? 5 polymer syn 'HCV IRES IIIABC' 17161.283 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GGCCGAGUAGUGUUGGGUCGCGAAAGGCC GGCCGAGUAGUGUUGGGUCGCGAAAGGCC A ? 2 polyribonucleotide no no GGCGCUCAAUGCUCUUCGGAGACGACCGCC GGCGCUCAAUGCUCUUCGGAGACGACCGCC B ? 3 polyribonucleotide no no GGCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGCC GGCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGCC C ? 4 polyribonucleotide no no CCCGGGGCCCGGGG CCCGGGGCCCGGGG D ? 5 polyribonucleotide no no GGCGGAACCGGUGAGUACACCGGAAUCCGAAAGGAUUUGGGCGUGCCCCCGCC GGCGGAACCGGUGAGUACACCGGAAUCCGAAAGGAUUUGGGCGUGCCCCCGCC E ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 C n 1 5 G n 1 6 A n 1 7 G n 1 8 U n 1 9 A n 1 10 G n 1 11 U n 1 12 G n 1 13 U n 1 14 U n 1 15 G n 1 16 G n 1 17 G n 1 18 U n 1 19 C n 1 20 G n 1 21 C n 1 22 G n 1 23 A n 1 24 A n 1 25 A n 1 26 G n 1 27 G n 1 28 C n 1 29 C n 2 1 G n 2 2 G n 2 3 C n 2 4 G n 2 5 C n 2 6 U n 2 7 C n 2 8 A n 2 9 A n 2 10 U n 2 11 G n 2 12 C n 2 13 U n 2 14 C n 2 15 U n 2 16 U n 2 17 C n 2 18 G n 2 19 G n 2 20 A n 2 21 G n 2 22 A n 2 23 C n 2 24 G n 2 25 A n 2 26 C n 2 27 C n 2 28 G n 2 29 C n 2 30 C n 3 1 G n 3 2 G n 3 3 C n 3 4 U n 3 5 G n 3 6 U n 3 7 G n 3 8 A n 3 9 G n 3 10 G n 3 11 A n 3 12 A n 3 13 C n 3 14 U n 3 15 A n 3 16 C n 3 17 U n 3 18 G n 3 19 U n 3 20 C n 3 21 U n 3 22 U n 3 23 C n 3 24 A n 3 25 C n 3 26 G n 3 27 C n 3 28 A n 3 29 G n 3 30 A n 3 31 A n 3 32 A n 3 33 G n 3 34 C n 3 35 G n 3 36 U n 3 37 C n 3 38 U n 3 39 A n 3 40 G n 3 41 C n 3 42 C n 3 43 A n 3 44 U n 3 45 G n 3 46 G n 3 47 C n 3 48 G n 3 49 U n 3 50 U n 3 51 A n 3 52 G n 3 53 U n 3 54 A n 3 55 U n 3 56 G n 3 57 A n 3 58 G n 3 59 U n 3 60 G n 3 61 U n 3 62 C n 3 63 G n 3 64 U n 3 65 G n 3 66 C n 3 67 A n 3 68 G n 3 69 C n 3 70 C n 3 71 U n 3 72 C n 3 73 C n 3 74 A n 3 75 G n 3 76 C n 3 77 C n 4 1 C n 4 2 C n 4 3 C n 4 4 G n 4 5 G n 4 6 G n 4 7 G n 4 8 C n 4 9 C n 4 10 C n 4 11 G n 4 12 G n 4 13 G n 4 14 G n 5 1 G n 5 2 G n 5 3 C n 5 4 G n 5 5 G n 5 6 A n 5 7 A n 5 8 C n 5 9 C n 5 10 G n 5 11 G n 5 12 U n 5 13 G n 5 14 A n 5 15 G n 5 16 U n 5 17 A n 5 18 C n 5 19 A n 5 20 C n 5 21 C n 5 22 G n 5 23 G n 5 24 A n 5 25 A n 5 26 U n 5 27 C n 5 28 C n 5 29 G n 5 30 A n 5 31 A n 5 32 A n 5 33 G n 5 34 G n 5 35 A n 5 36 U n 5 37 U n 5 38 U n 5 39 G n 5 40 G n 5 41 G n 5 42 C n 5 43 G n 5 44 U n 5 45 G n 5 46 C n 5 47 C n 5 48 C n 5 49 C n 5 50 C n 5 51 G n 5 52 C n 5 53 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'synthetic construct' ? 32630 ? 2 1 sample ? ? 'synthetic construct' ? 32630 ? 3 1 sample ? ? 'synthetic construct' ? 32630 ? 4 1 sample ? ? 'synthetic construct' ? 32630 ? 5 1 sample ? ? 'synthetic construct' ? 32630 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 ? ? ? A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 U 11 11 11 U U A . n A 1 12 G 12 12 12 G G A . n A 1 13 U 13 13 13 U U A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 G 16 16 16 G G A . n A 1 17 G 17 17 17 G G A . n A 1 18 U 18 18 18 U U A . n A 1 19 C 19 19 19 C C A . n A 1 20 G 20 20 20 G G A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 A 23 23 23 A A A . n A 1 24 A 24 24 24 A A A . n A 1 25 A 25 25 25 A A A . n A 1 26 G 26 26 26 G G A . n A 1 27 G 27 27 27 G G A . n A 1 28 C 28 28 28 C C A . n A 1 29 C 29 29 29 C C A . n B 2 1 G 1 1 ? ? ? B . n B 2 2 G 2 2 2 G G B . n B 2 3 C 3 3 3 C C B . n B 2 4 G 4 4 4 G G B . n B 2 5 C 5 5 5 C C B . n B 2 6 U 6 6 6 U U B . n B 2 7 C 7 7 7 C C B . n B 2 8 A 8 8 8 A A B . n B 2 9 A 9 9 9 A A B . n B 2 10 U 10 10 10 U U B . n B 2 11 G 11 11 11 G G B . n B 2 12 C 12 12 12 C C B . n B 2 13 U 13 13 13 U U B . n B 2 14 C 14 14 14 C C B . n B 2 15 U 15 15 ? ? ? B . n B 2 16 U 16 16 ? ? ? B . n B 2 17 C 17 17 ? ? ? B . n B 2 18 G 18 18 ? ? ? B . n B 2 19 G 19 19 19 G G B . n B 2 20 A 20 20 20 A A B . n B 2 21 G 21 21 21 G G B . n B 2 22 A 22 22 22 A A B . n B 2 23 C 23 23 23 C C B . n B 2 24 G 24 24 24 G G B . n B 2 25 A 25 25 25 A A B . n B 2 26 C 26 26 26 C C B . n B 2 27 C 27 27 27 C C B . n B 2 28 G 28 28 28 G G B . n B 2 29 C 29 29 29 C C B . n B 2 30 C 30 30 30 C C B . n C 3 1 G 1 1 ? ? ? C . n C 3 2 G 2 2 2 G G C . n C 3 3 C 3 3 3 C C C . n C 3 4 U 4 4 4 U U C . n C 3 5 G 5 5 5 G G C . n C 3 6 U 6 6 6 U U C . n C 3 7 G 7 7 7 G G C . n C 3 8 A 8 8 8 A A C . n C 3 9 G 9 9 9 G G C . n C 3 10 G 10 10 10 G G C . n C 3 11 A 11 11 11 A A C . n C 3 12 A 12 12 12 A A C . n C 3 13 C 13 13 13 C C C . n C 3 14 U 14 14 14 U U C . n C 3 15 A 15 15 15 A A C . n C 3 16 C 16 16 16 C C C . n C 3 17 U 17 17 17 U U C . n C 3 18 G 18 18 18 G G C . n C 3 19 U 19 19 19 U U C . n C 3 20 C 20 20 20 C C C . n C 3 21 U 21 21 21 U U C . n C 3 22 U 22 22 22 U U C . n C 3 23 C 23 23 23 C C C . n C 3 24 A 24 24 24 A A C . n C 3 25 C 25 25 25 C C C . n C 3 26 G 26 26 26 G G C . n C 3 27 C 27 27 27 C C C . n C 3 28 A 28 28 28 A A C . n C 3 29 G 29 29 29 G G C . n C 3 30 A 30 30 30 A A C . n C 3 31 A 31 31 31 A A C . n C 3 32 A 32 32 32 A A C . n C 3 33 G 33 33 33 G G C . n C 3 34 C 34 34 34 C C C . n C 3 35 G 35 35 35 G G C . n C 3 36 U 36 36 36 U U C . n C 3 37 C 37 37 37 C C C . n C 3 38 U 38 38 38 U U C . n C 3 39 A 39 39 39 A A C . n C 3 40 G 40 40 40 G G C . n C 3 41 C 41 41 41 C C C . n C 3 42 C 42 42 42 C C C . n C 3 43 A 43 43 43 A A C . n C 3 44 U 44 44 44 U U C . n C 3 45 G 45 45 45 G G C . n C 3 46 G 46 46 46 G G C . n C 3 47 C 47 47 47 C C C . n C 3 48 G 48 48 48 G G C . n C 3 49 U 49 49 49 U U C . n C 3 50 U 50 50 50 U U C . n C 3 51 A 51 51 51 A A C . n C 3 52 G 52 52 52 G G C . n C 3 53 U 53 53 53 U U C . n C 3 54 A 54 54 54 A A C . n C 3 55 U 55 55 55 U U C . n C 3 56 G 56 56 56 G G C . n C 3 57 A 57 57 57 A A C . n C 3 58 G 58 58 58 G G C . n C 3 59 U 59 59 59 U U C . n C 3 60 G 60 60 60 G G C . n C 3 61 U 61 61 61 U U C . n C 3 62 C 62 62 62 C C C . n C 3 63 G 63 63 63 G G C . n C 3 64 U 64 64 64 U U C . n C 3 65 G 65 65 65 G G C . n C 3 66 C 66 66 66 C C C . n C 3 67 A 67 67 67 A A C . n C 3 68 G 68 68 68 G G C . n C 3 69 C 69 69 69 C C C . n C 3 70 C 70 70 70 C C C . n C 3 71 U 71 71 71 U U C . n C 3 72 C 72 72 72 C C C . n C 3 73 C 73 73 73 C C C . n C 3 74 A 74 74 74 A A C . n C 3 75 G 75 75 75 G G C . n C 3 76 C 76 76 76 C C C . n C 3 77 C 77 77 77 C C C . n D 4 1 C 1 2 2 C C D . n D 4 2 C 2 3 3 C C D . n D 4 3 C 3 4 4 C C D . n D 4 4 G 4 5 5 G G D . n D 4 5 G 5 6 6 G G D . n D 4 6 G 6 7 7 G G D . n D 4 7 G 7 8 8 G G D . n D 4 8 C 8 9 9 C C D . n D 4 9 C 9 10 10 C C D . n D 4 10 C 10 11 11 C C D . n D 4 11 G 11 12 12 G G D . n D 4 12 G 12 13 13 G G D . n D 4 13 G 13 14 14 G G D . n D 4 14 G 14 15 15 G G D . n E 5 1 G 1 1 ? ? ? E . n E 5 2 G 2 2 2 G G E . n E 5 3 C 3 3 3 C C E . n E 5 4 G 4 4 4 G G E . n E 5 5 G 5 5 5 G G E . n E 5 6 A 6 6 6 A A E . n E 5 7 A 7 7 7 A A E . n E 5 8 C 8 8 8 C C E . n E 5 9 C 9 9 9 C C E . n E 5 10 G 10 10 10 G G E . n E 5 11 G 11 11 ? ? ? E . n E 5 12 U 12 12 ? ? ? E . n E 5 13 G 13 13 ? ? ? E . n E 5 14 A 14 14 ? ? ? E . n E 5 15 G 15 15 ? ? ? E . n E 5 16 U 16 16 ? ? ? E . n E 5 17 A 17 17 17 A A E . n E 5 18 C 18 18 18 C C E . n E 5 19 A 19 19 19 A A E . n E 5 20 C 20 20 20 C C E . n E 5 21 C 21 21 21 C C E . n E 5 22 G 22 22 22 G G E . n E 5 23 G 23 23 23 G G E . n E 5 24 A 24 24 24 A A E . n E 5 25 A 25 25 25 A A E . n E 5 26 U 26 26 26 U U E . n E 5 27 C 27 27 27 C C E . n E 5 28 C 28 28 28 C C E . n E 5 29 G 29 29 ? ? ? E . n E 5 30 A 30 30 ? ? ? E . n E 5 31 A 31 31 ? ? ? E . n E 5 32 A 32 32 ? ? ? E . n E 5 33 G 33 33 33 G G E . n E 5 34 G 34 34 34 G G E . n E 5 35 A 35 35 35 A A E . n E 5 36 U 36 36 36 U U E . n E 5 37 U 37 37 37 U U E . n E 5 38 U 38 38 38 U U E . n E 5 39 G 39 39 39 G G E . n E 5 40 G 40 40 40 G G E . n E 5 41 G 41 41 41 G G E . n E 5 42 C 42 42 42 C C E . n E 5 43 G 43 43 43 G G E . n E 5 44 U 44 44 ? ? ? E . n E 5 45 G 45 45 45 G G E . n E 5 46 C 46 46 46 C C E . n E 5 47 C 47 47 47 C C E . n E 5 48 C 48 48 48 C C E . n E 5 49 C 49 49 49 C C E . n E 5 50 C 50 50 50 C C E . n E 5 51 G 51 51 51 G G E . n E 5 52 C 52 52 52 C C E . n E 5 53 C 53 53 ? ? ? E . n # _cell.entry_id 2AGN _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2AGN _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 2AGN _exptl.method 'ELECTRON MICROSCOPY' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 183 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 183 _refine_hist.d_res_high . _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 2AGN _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2AGN _struct.title ;Fitting of hepatitis C virus internal ribosome entry site domains into the 15 A Cryo-EM map of a HCV IRES-80S ribosome (H. sapiens) complex ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2AGN _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HCV, IRES, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 2AGN 2AGN ? ? ? 2 2 PDB 2AGN 2AGN ? ? ? 3 3 PDB 2AGN 2AGN ? ? ? 4 4 PDB 2AGN 2AGN ? ? ? 5 5 PDB 2AGN 2AGN ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2AGN A 1 ? 29 ? 2AGN 1 ? 29 ? 1 29 2 2 2AGN B 1 ? 30 ? 2AGN 1 ? 30 ? 1 30 3 3 2AGN C 1 ? 77 ? 2AGN 1 ? 77 ? 1 77 4 4 2AGN D 1 ? 14 ? 2AGN 2 ? 15 ? 2 15 5 5 2AGN E 1 ? 53 ? 2AGN 1 ? 53 ? 1 53 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 2AGN _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space REAL _em_3d_fitting.overall_b_value ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.method ? # loop_ _em_3d_fitting_list.3d_fitting_id _em_3d_fitting_list.id _em_3d_fitting_list.pdb_entry_id _em_3d_fitting_list.pdb_chain_id _em_3d_fitting_list.details _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.chain_id _em_3d_fitting_list.chain_residue_range _em_3d_fitting_list.pdb_chain_residue_range _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_3d_fitting_list.accession_code 1 1 1P5P ? ? 1 ? ? ? PDB 'experimental model' 1P5P 1 2 1F84 ? ? 2 ? ? ? PDB 'experimental model' 1F84 1 3 1KH6 ? ? 3 ? ? ? PDB 'experimental model' 1KH6 1 4 1KP7 ? ? 4 ? ? ? PDB 'experimental model' 1KP7 # _em_3d_reconstruction.entry_id 2AGN _em_3d_reconstruction.id 1 _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.num_particles 24100 _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.method 'angular reconstitution' _em_3d_reconstruction.nominal_pixel_size 3.6 _em_3d_reconstruction.actual_pixel_size 3.6 _em_3d_reconstruction.resolution 15 _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.details 'This entry contains only phosphorus atom in the coordinate.' _em_3d_reconstruction.resolution_method ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.refinement_type ? # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.pH 8.1 _em_buffer.details ? # _em_entity_assembly.id 1 _em_entity_assembly.name 'HCV IRES-80S ribosome complex' _em_entity_assembly.type RIBOSOME _em_entity_assembly.parent_id 0 _em_entity_assembly.synonym ? _em_entity_assembly.details ? _em_entity_assembly.oligomeric_details ? # _em_imaging.entry_id 2AGN _em_imaging.id 1 _em_imaging.microscope_model 'FEI/PHILIPS CM200FEG' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.specimen_id 1 _em_imaging.date 2003-10-01 _em_imaging.temperature 77 _em_imaging.nominal_defocus_min 2000 _em_imaging.nominal_defocus_max 4000 _em_imaging.tilt_angle_min 0 _em_imaging.tilt_angle_max 0 _em_imaging.nominal_cs 2 _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_magnification 50000 _em_imaging.calibrated_magnification 50000 _em_imaging.accelerating_voltage 200 _em_imaging.details ? _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.citation_id ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details 'perforated corbon foil on a copper grid' _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? _em_sample_support.method ? # _em_vitrification.entry_id 2AGN _em_vitrification.id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.details 'plunging into liquid ethane' _em_vitrification.citation_id ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.specimen_id 1 _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 2AGN _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' # _em_single_particle_entity.entry_id 2AGN _em_single_particle_entity.id 1 _em_single_particle_entity.point_symmetry C1 _em_single_particle_entity.image_processing_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A G 1 ? A G 1 2 1 Y 1 B G 1 ? B G 1 3 1 Y 1 B U 15 ? B U 15 4 1 Y 1 B U 16 ? B U 16 5 1 Y 1 B C 17 ? B C 17 6 1 Y 1 B G 18 ? B G 18 7 1 Y 1 C G 1 ? C G 1 8 1 Y 1 E G 1 ? E G 1 9 1 Y 1 E G 11 ? E G 11 10 1 Y 1 E U 12 ? E U 12 11 1 Y 1 E G 13 ? E G 13 12 1 Y 1 E A 14 ? E A 14 13 1 Y 1 E G 15 ? E G 15 14 1 Y 1 E U 16 ? E U 16 15 1 Y 1 E G 29 ? E G 29 16 1 Y 1 E A 30 ? E A 30 17 1 Y 1 E A 31 ? E A 31 18 1 Y 1 E A 32 ? E A 32 19 1 Y 1 E U 44 ? E U 44 20 1 Y 1 E C 53 ? E C 53 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 U OP3 O N N 111 U P P N N 112 U OP1 O N N 113 U OP2 O N N 114 U "O5'" O N N 115 U "C5'" C N N 116 U "C4'" C N R 117 U "O4'" O N N 118 U "C3'" C N S 119 U "O3'" O N N 120 U "C2'" C N R 121 U "O2'" O N N 122 U "C1'" C N R 123 U N1 N N N 124 U C2 C N N 125 U O2 O N N 126 U N3 N N N 127 U C4 C N N 128 U O4 O N N 129 U C5 C N N 130 U C6 C N N 131 U HOP3 H N N 132 U HOP2 H N N 133 U "H5'" H N N 134 U "H5''" H N N 135 U "H4'" H N N 136 U "H3'" H N N 137 U "HO3'" H N N 138 U "H2'" H N N 139 U "HO2'" H N N 140 U "H1'" H N N 141 U H3 H N N 142 U H5 H N N 143 U H6 H N N 144 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # _em_ctf_correction.id 1 _em_ctf_correction.details 'phase reversal' _em_ctf_correction.type . _em_ctf_correction.em_image_processing_id ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.details 'Kodak SO-163' _em_image_recording.id 1 _em_image_recording.avg_electron_dose_per_image 20 _em_image_recording.film_or_detector_model 'GENERIC FILM' _em_image_recording.imaging_id 1 _em_image_recording.detector_mode ? _em_image_recording.average_exposure_time ? _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.id _em_software.name _em_software.version _em_software.category _em_software.details _em_software.image_processing_id 1 IMAGIC ? RECONSTRUCTION ? 1 2 Amira 2.3 'MODEL FITTING' ? ? # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration ? _em_specimen.vitrification_applied YES _em_specimen.staining_applied NO _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details ? # loop_ _pdbx_coordinate_model.asym_id _pdbx_coordinate_model.type A 'P ATOMS ONLY' B 'P ATOMS ONLY' C 'P ATOMS ONLY' D 'P ATOMS ONLY' E 'P ATOMS ONLY' # loop_ _pdbx_initial_refinement_model.id _pdbx_initial_refinement_model.type _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.accession_code 1 'experimental model' PDB 1P5P 2 'experimental model' PDB 1F84 3 'experimental model' PDB 1KH6 4 'experimental model' PDB 1KP7 # _atom_sites.entry_id 2AGN _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # _atom_type.symbol P # loop_