data_9A9I # _entry.id 9A9I # loop_ _atom_type.symbol C H N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Williams, R.V." 1 "Gierasch, L.M." 2 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.28 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.403 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A9I _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2025-02-28 # 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 2026-09-02 # _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 ? # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9A9I pdb_00009a9i 10.2210/pdb9a9i/pdb # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.094 ALA . ALANINE . "L-peptide linking" "C6 H15 N4 O2 1" 175.212 ARG . ARGININE . "L-peptide linking" "C4 H8 N2 O3" 132.119 ASN . ASPARAGINE . "L-peptide linking" "C4 H7 N O4" 133.103 ASP . "ASPARTIC ACID" . "L-peptide linking" "C3 H7 N O2 S" 121.154 CYS . CYSTEINE . "L-peptide linking" "C5 H10 N2 O3" 146.146 GLN . GLUTAMINE . "L-peptide linking" "C5 H9 N O4" 147.13 GLU . "GLUTAMIC ACID" . "L-peptide linking" "C2 H5 N O2" 75.067 GLY . GLYCINE . "peptide linking" "C6 H13 N O2" 131.175 LEU . LEUCINE . "L-peptide linking" "C6 H15 N2 O2 1" 147.198 LYS . LYSINE . "L-peptide linking" "C9 H11 N O2" 165.192 PHE . PHENYLALANINE . "L-peptide linking" "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C3 H7 N O3" 105.093 SER . SERINE . "L-peptide linking" "C4 H9 N O3" 119.12 THR . THREONINE . "L-peptide linking" # _citation.country . _citation.id 1 _citation.journal_abbrev bioRxiv _citation.journal_id_ASTM . _citation.journal_id_CSD . _citation.journal_id_ISSN . _citation.journal_issue . _citation.journal_volume . _citation.page_first . _citation.page_last . _citation.pdbx_database_id_DOI 10.1101/2025.08.11.669745 _citation.pdbx_database_id_PubMed 40832263 _citation.title "The cysteine-rich domain of SEP15, a selenoprotein co-chaperone of the ER chaperone, UDP-glucose:glycoprotein glucosyltransferase, adopts a novel fold" _citation.year 2025 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Williams, R.V." 1 1 "Guay, K.P." 2 1 "Hurlbut Lesk, O." 3 1 "Hebert, D.N." 4 1 "Gierasch, L.M." 5 # _entity.details . _entity.formula_weight 6663.177 _entity.id 1 _entity.pdbx_description "Selenoprotein F cysteine-rich domain" _entity.pdbx_number_of_molecules 1 _entity.src_method MAN _entity.type POLYMER # _entity_name_com.entity_id 1 _entity_name_com.name SEP15 # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer NO _entity_poly.pdbx_seq_one_letter_code FGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETK _entity_poly.pdbx_seq_one_letter_code_can FGAEFSSEACRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGCCQEEAQFETK _entity_poly.pdbx_sequence_evidence_code . _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 . PHE 1 1 . GLY 2 1 . ALA 3 1 . GLU 4 1 . PHE 5 1 . SER 6 1 . SER 7 1 . GLU 8 1 . ALA 9 1 . CYS 10 1 . ARG 11 1 . GLU 12 1 . LEU 13 1 . GLY 14 1 . PHE 15 1 . SER 16 1 . SER 17 1 . ASN 18 1 . LEU 19 1 . LEU 20 1 . CYS 21 1 . SER 22 1 . SER 23 1 . CYS 24 1 . ASP 25 1 . LEU 26 1 . LEU 27 1 . GLY 28 1 . GLN 29 1 . PHE 30 1 . ASN 31 1 . LEU 32 1 . LEU 33 1 . GLN 34 1 . LEU 35 1 . ASP 36 1 . PRO 37 1 . ASP 38 1 . CYS 39 1 . ARG 40 1 . GLY 41 1 . CYS 42 1 . CYS 43 1 . GLN 44 1 . GLU 45 1 . GLU 46 1 . ALA 47 1 . GLN 48 1 . PHE 49 1 . GLU 50 1 . THR 51 1 . LYS 52 # _ihm_dataset_group.application modeling _ihm_dataset_group.details "Chemical shifts & RDCs" _ihm_dataset_group.id 1 _ihm_dataset_group.name . # _ihm_dataset_group_link.dataset_list_id 1 _ihm_dataset_group_link.group_id 1 # _ihm_dataset_list.data_type "NMR data" _ihm_dataset_list.database_hosted YES _ihm_dataset_list.details "Backbone chemical shifts and Backbone N-H residual dipolar couplings" _ihm_dataset_list.id 1 # _ihm_dataset_related_db_reference.accession_code 52892 _ihm_dataset_related_db_reference.dataset_list_id 1 _ihm_dataset_related_db_reference.db_name BMRB _ihm_dataset_related_db_reference.details . _ihm_dataset_related_db_reference.id 1 _ihm_dataset_related_db_reference.version . # _ihm_entity_poly_segment.comp_id_begin PHE _ihm_entity_poly_segment.comp_id_end LYS _ihm_entity_poly_segment.entity_id 1 _ihm_entity_poly_segment.id 1 _ihm_entity_poly_segment.seq_id_begin 1 _ihm_entity_poly_segment.seq_id_end 52 # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 # loop_ _ihm_model_list.assembly_id _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 1 . 1 1 1 2 . 1 1 1 3 . 1 1 1 4 . 1 1 1 5 . 1 1 1 6 . 1 1 1 7 . 1 1 1 8 . 1 1 1 9 . 1 1 1 10 . 1 1 # _ihm_model_representation.details "No starting models were used" _ihm_model_representation.id 1 _ihm_model_representation.name . # _ihm_model_representation_details.description . _ihm_model_representation_details.entity_asym_id A _ihm_model_representation_details.entity_description . _ihm_model_representation_details.entity_id 1 _ihm_model_representation_details.entity_poly_segment_id 1 _ihm_model_representation_details.id 1 _ihm_model_representation_details.model_granularity by-atom _ihm_model_representation_details.model_mode flexible _ihm_model_representation_details.model_object_count . _ihm_model_representation_details.model_object_primitive atomistic _ihm_model_representation_details.representation_id 1 _ihm_model_representation_details.starting_model_id . # _ihm_model_representative.id 1 _ihm_model_representative.model_group_id 1 _ihm_model_representative.model_id 1 _ihm_model_representative.selection_criteria "lowest energy" # _ihm_modeling_post_process.analysis_id 1 _ihm_modeling_post_process.dataset_group_id 1 _ihm_modeling_post_process.details . _ihm_modeling_post_process.feature energy/score _ihm_modeling_post_process.feature_name "Ten lowest energy structures" _ihm_modeling_post_process.id 1 _ihm_modeling_post_process.num_models_begin 3000 _ihm_modeling_post_process.num_models_end 10 _ihm_modeling_post_process.protocol_id 1 _ihm_modeling_post_process.script_file_id . _ihm_modeling_post_process.software_id 1 _ihm_modeling_post_process.step_id 1 _ihm_modeling_post_process.struct_assembly_id 1 _ihm_modeling_post_process.type filter # _ihm_modeling_protocol.details "Selenoprotein F modeled using CS-Rosetta, guided by its experimentally determined chemical shift values and amide N-H residual dipolar couplings" _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name CS-Rosetta # _ihm_modeling_protocol_details.dataset_group_id 1 _ihm_modeling_protocol_details.description . _ihm_modeling_protocol_details.ensemble_flag YES _ihm_modeling_protocol_details.id 1 _ihm_modeling_protocol_details.multi_scale_flag NO _ihm_modeling_protocol_details.multi_state_flag NO _ihm_modeling_protocol_details.num_models_begin 0 _ihm_modeling_protocol_details.num_models_end 3000 _ihm_modeling_protocol_details.ordered_flag NO _ihm_modeling_protocol_details.protocol_id 1 _ihm_modeling_protocol_details.script_file_id . _ihm_modeling_protocol_details.software_id 1 _ihm_modeling_protocol_details.step_id 1 _ihm_modeling_protocol_details.step_method CS-Rosetta _ihm_modeling_protocol_details.step_name 1 _ihm_modeling_protocol_details.struct_assembly_description . _ihm_modeling_protocol_details.struct_assembly_id 1 # loop_ _ihm_residues_not_modeled.asym_id _ihm_residues_not_modeled.comp_id_begin _ihm_residues_not_modeled.comp_id_end _ihm_residues_not_modeled.details _ihm_residues_not_modeled.entity_description _ihm_residues_not_modeled.entity_id _ihm_residues_not_modeled.id _ihm_residues_not_modeled.model_id _ihm_residues_not_modeled.reason _ihm_residues_not_modeled.seq_id_begin _ihm_residues_not_modeled.seq_id_end A PHE PHE . . 1 1 1 . 1 5 A GLU LYS . . 1 2 1 . 45 52 A PHE PHE . . 1 3 2 . 1 5 A GLU LYS . . 1 4 2 . 45 52 A PHE PHE . . 1 5 3 . 1 5 A GLU LYS . . 1 6 3 . 45 52 A PHE PHE . . 1 7 4 . 1 5 A GLU LYS . . 1 8 4 . 45 52 A PHE PHE . . 1 9 5 . 1 5 A GLU LYS . . 1 10 5 . 45 52 A PHE PHE . . 1 11 6 . 1 5 A GLU LYS . . 1 12 6 . 45 52 A PHE PHE . . 1 13 7 . 1 5 A GLU LYS . . 1 14 7 . 45 52 A PHE PHE . . 1 15 8 . 1 5 A GLU LYS . . 1 16 8 . 45 52 A PHE PHE . . 1 17 9 . 1 5 A GLU LYS . . 1 18 9 . 45 52 A PHE PHE . . 1 19 10 . 1 5 A GLU LYS . . 1 20 10 . 45 52 # _ihm_struct_assembly.description "CS-rosetta structure of Selenoprotein F cysteine-rich domain modeled using NMR backbone chemical shifts and amide N-H residual dipolar couplings" _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "Selenoprotein F cysteine-rich domain" # _ihm_struct_assembly_details.assembly_id 1 _ihm_struct_assembly_details.asym_id A _ihm_struct_assembly_details.entity_description . _ihm_struct_assembly_details.entity_id 1 _ihm_struct_assembly_details.entity_poly_segment_id 1 _ihm_struct_assembly_details.id 1 _ihm_struct_assembly_details.parent_assembly_id 1 # _software.citation_id . _software.classification "model building" _software.description "Integrative modelling" _software.location https://www.rosettacommons.org/docs/latest/CS-Rosetta _software.name CS-Rosetta _software.pdbx_ordinal 1 _software.type program _software.version . # _struct.entry_id 9A9I _struct.pdbx_CASP_flag . _struct.pdbx_descriptor . _struct.pdbx_details . _struct.pdbx_model_details . _struct.pdbx_model_type_details . _struct.pdbx_structure_determination_methodology integrative _struct.title "CS-Rosetta model of the cysteine-rich domain of the 15-kDa selenoprotein (SEP15) using backbone chemical shifts and residual dipolar couplings" # _struct_asym.details . _struct_asym.entity_id 1 _struct_asym.id A _struct_asym.pdbx_PDB_id . _struct_asym.pdbx_alt_id . _struct_asym.pdbx_blank_PDB_chainid_flag . _struct_asym.pdbx_modified . _struct_asym.pdbx_order . _struct_asym.pdbx_type . # _struct_ref.db_code SEP15_HUMAN _struct_ref.db_name UNP _struct_ref.details . _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 32 _struct_ref.pdbx_align_end 83 _struct_ref.pdbx_db_accession O60613 _struct_ref.pdbx_db_isoform . _struct_ref.pdbx_seq_one_letter_code . # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 32 _struct_ref_seq.db_align_end 83 _struct_ref_seq.details . _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 52 # 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.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 A 1 1 PHE -4 ? ? ? A . A 1 2 GLY -3 ? ? ? A . A 1 3 ALA -2 ? ? ? A . A 1 4 GLU -1 ? ? ? A . A 1 5 PHE 0 ? ? ? A . A 1 6 SER 1 1 SER SER A ? A 1 7 SER 2 2 SER SER A ? A 1 8 GLU 3 3 GLU GLU A ? A 1 9 ALA 4 4 ALA ALA A ? A 1 10 CYS 5 5 CYS CYS A ? A 1 11 ARG 6 6 ARG ARG A ? A 1 12 GLU 7 7 GLU GLU A ? A 1 13 LEU 8 8 LEU LEU A ? A 1 14 GLY 9 9 GLY GLY A ? A 1 15 PHE 10 10 PHE PHE A ? A 1 16 SER 11 11 SER SER A ? A 1 17 SER 12 12 SER SER A ? A 1 18 ASN 13 13 ASN ASN A ? A 1 19 LEU 14 14 LEU LEU A ? A 1 20 LEU 15 15 LEU LEU A ? A 1 21 CYS 16 16 CYS CYS A ? A 1 22 SER 17 17 SER SER A ? A 1 23 SER 18 18 SER SER A ? A 1 24 CYS 19 19 CYS CYS A ? A 1 25 ASP 20 20 ASP ASP A ? A 1 26 LEU 21 21 LEU LEU A ? A 1 27 LEU 22 22 LEU LEU A ? A 1 28 GLY 23 23 GLY GLY A ? A 1 29 GLN 24 24 GLN GLN A ? A 1 30 PHE 25 25 PHE PHE A ? A 1 31 ASN 26 26 ASN ASN A ? A 1 32 LEU 27 27 LEU LEU A ? A 1 33 LEU 28 28 LEU LEU A ? A 1 34 GLN 29 29 GLN GLN A ? A 1 35 LEU 30 30 LEU LEU A ? A 1 36 ASP 31 31 ASP ASP A ? A 1 37 PRO 32 32 PRO PRO A ? A 1 38 ASP 33 33 ASP ASP A ? A 1 39 CYS 34 34 CYS CYS A ? A 1 40 ARG 35 35 ARG ARG A ? A 1 41 GLY 36 36 GLY GLY A ? A 1 42 CYS 37 37 CYS CYS A ? A 1 43 CYS 38 38 CYS CYS A ? A 1 44 GLN 39 39 GLN GLN A ? A 1 45 GLU 40 ? ? ? A . A 1 46 GLU 41 ? ? ? A . A 1 47 ALA 42 ? ? ? A . A 1 48 GLN 43 ? ? ? A . A 1 49 PHE 44 ? ? ? A . A 1 50 GLU 45 ? ? ? A . A 1 51 THR 46 ? ? ? A . A 1 52 LYS 47 ? ? ? A . # # loop_ # #