data_5AEF # _entry.id 5AEF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.315 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5AEF PDBE EBI-64853 WWPDB D_1290064853 # _pdbx_database_related.db_name EMDB _pdbx_database_related.db_id EMD-3132 _pdbx_database_related.content_type 'associated EM volume' _pdbx_database_related.details . # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 5AEF _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2015-08-29 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Schmidt, M.' 1 'Rohou, A.' 2 'Lasker, K.' 3 'Yadav, J.K.' 4 'Schiene-Fischer, C.' 5 'Fandrich, M.' 6 'Grigorieff, N.' 7 # _citation.id primary _citation.title 'Peptide Dimer Structure in an Abeta(1-42) Fibril Visualized with Cryo-Em' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 112 _citation.page_first 11858 _citation.page_last ? _citation.year 2015 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26351699 _citation.pdbx_database_id_DOI 10.1073/PNAS.1503455112 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schmidt, M.' 1 ? primary 'Rohou, A.' 2 ? primary 'Lasker, K.' 3 ? primary 'Yadav, J.K.' 4 ? primary 'Schiene-Fischer, C.' 5 ? primary 'Fandrich, M.' 6 ? primary 'Grigorie, N.' 7 ? # _cell.entry_id 5AEF _cell.length_a 1.0 _cell.length_b 1.0 _cell.length_c 1.0 _cell.angle_alpha 90.0 _cell.angle_beta 90.0 _cell.angle_gamma 90.0 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AEF _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'AMYLOID BETA A4 PROTEIN' _entity.formula_weight 2835.365 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'ABETA, UNP RESIDUES 630-657' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name ABETA17-42 # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code QKLVFFAEDVGSNKGAIIGLMVGGVVIA _entity_poly.pdbx_seq_one_letter_code_can QKLVFFAEDVGSNKGAIIGLMVGGVVIA _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLN n 1 2 LYS n 1 3 LEU n 1 4 VAL n 1 5 PHE n 1 6 PHE n 1 7 ALA n 1 8 GLU n 1 9 ASP n 1 10 VAL n 1 11 GLY n 1 12 SER n 1 13 ASN n 1 14 LYS n 1 15 GLY n 1 16 ALA n 1 17 ILE n 1 18 ILE n 1 19 GLY n 1 20 LEU n 1 21 MET n 1 22 VAL n 1 23 GLY n 1 24 GLY n 1 25 VAL n 1 26 VAL n 1 27 ILE n 1 28 ALA n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'HOMO SAPIENS' _pdbx_entity_src_syn.organism_common_name HUMAN _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code E9PG40_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession E9PG40 _struct_ref.pdbx_db_isoform ? # 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 5AEF A 1 ? 28 ? E9PG40 630 ? 657 ? 15 42 2 1 5AEF B 1 ? 28 ? E9PG40 630 ? 657 ? 15 42 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 5AEF _exptl.method 'ELECTRON MICROSCOPY' _exptl.crystals_number ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 5AEF _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high 5.00 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 388 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 388 _refine_hist.d_res_high 5.00 _refine_hist.d_res_low . # _struct.entry_id 5AEF _struct.title 'Electron cryo-microscopy of an Abeta(1-42)amyloid fibril' _struct.pdbx_descriptor 'AMYLOID BETA A4 PROTEIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5AEF _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' _struct_keywords.text ;PROTEIN FIBRIL, ALZHEIMER'S DISEASE, AMYLOID FIBRIL, PROTEIN AGGREGATION, PROTEIN FOLDING, CROSS-BETA, FREALIX ; # 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 1 ? # _struct_biol.id 1 # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLY 23 A . ? GLY 37 A GLY 24 A ? GLY 38 A 1 -25.15 2 GLY 23 B . ? GLY 37 B GLY 24 B ? GLY 38 B 1 -28.66 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 2 ? AC ? 2 ? AD ? 2 ? BA ? 4 ? BB ? 2 ? BC ? 2 ? BD ? 4 ? BE ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? parallel AB 1 2 ? parallel AC 1 2 ? parallel AD 1 2 ? parallel BA 1 2 ? parallel BA 2 3 ? anti-parallel BA 3 4 ? anti-parallel BB 1 2 ? parallel BC 1 2 ? parallel BD 1 2 ? parallel BD 2 3 ? parallel BD 3 4 ? parallel BE 1 2 ? parallel BE 2 3 ? parallel BE 3 4 ? parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 LYS A 2 ? VAL A 4 ? LYS A 16 VAL A 18 AA 2 LEU A 3 ? PHE A 5 ? LEU A 17 PHE A 19 AB 1 GLY A 19 ? LEU A 20 ? GLY A 33 LEU A 34 AB 2 ALA A 16 ? GLY A 23 ? ALA A 30 GLY A 37 AC 1 ALA A 16 ? ILE A 18 ? ALA A 30 ILE A 32 AC 2 ALA A 16 ? GLY A 23 ? ALA A 30 GLY A 37 AD 1 MET A 21 ? VAL A 26 ? MET A 35 VAL A 40 AD 2 ALA A 16 ? GLY A 23 ? ALA A 30 GLY A 37 BA 1 LYS B 2 ? PHE B 5 ? LYS B 16 PHE B 19 BA 2 LEU B 3 ? PHE B 6 ? LEU B 17 PHE B 20 BA 3 PHE B 5 ? PHE B 6 ? PHE B 19 PHE B 20 BA 4 LYS B 2 ? PHE B 5 ? LYS B 16 PHE B 19 BB 1 ASN B 13 ? LYS B 14 ? ASN B 27 LYS B 28 BB 2 ASN B 13 ? LEU B 20 ? ASN B 27 LEU B 34 BC 1 ILE B 18 ? GLY B 19 ? ILE B 32 GLY B 33 BC 2 ASN B 13 ? LEU B 20 ? ASN B 27 LEU B 34 BD 1 MET B 21 ? VAL B 22 ? MET B 35 VAL B 36 BD 2 LYS B 14 ? VAL B 22 ? LYS B 28 VAL B 36 BD 3 ASN B 13 ? LEU B 20 ? ASN B 27 LEU B 34 BD 4 ILE B 18 ? GLY B 19 ? ILE B 32 GLY B 33 BE 1 MET B 21 ? VAL B 22 ? MET B 35 VAL B 36 BE 2 LYS B 14 ? VAL B 22 ? LYS B 28 VAL B 36 BE 3 ASN B 13 ? LEU B 20 ? ASN B 27 LEU B 34 BE 4 ASN B 13 ? LYS B 14 ? ASN B 27 LYS B 28 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N LEU A 3 ? N LEU A 17 O LEU A 3 ? O LEU A 17 AB 1 2 N LEU A 20 ? N LEU A 34 O GLY A 19 ? O GLY A 33 AC 1 2 N ILE A 17 ? N ILE A 31 O ALA A 16 ? O ALA A 30 AD 1 2 N VAL A 22 ? N VAL A 36 O MET A 21 ? O MET A 35 BA 1 2 N LEU B 3 ? N LEU B 17 O LEU B 3 ? O LEU B 17 BA 2 3 N PHE B 5 ? N PHE B 19 O PHE B 5 ? O PHE B 19 BA 3 4 N PHE B 5 ? N PHE B 19 O LEU B 3 ? O LEU B 17 BB 1 2 N LYS B 14 ? N LYS B 28 O ASN B 13 ? O ASN B 27 BC 1 2 N ILE B 18 ? N ILE B 32 O ILE B 17 ? O ILE B 31 BD 1 2 N MET B 21 ? N MET B 35 O MET B 21 ? O MET B 35 BD 2 3 N LYS B 14 ? N LYS B 28 O ASN B 13 ? O ASN B 27 BD 3 4 N GLY B 19 ? N GLY B 33 O ILE B 18 ? O ILE B 32 BE 1 2 N MET B 21 ? N MET B 35 O MET B 21 ? O MET B 35 BE 2 3 N LYS B 14 ? N LYS B 28 O ASN B 13 ? O ASN B 27 BE 3 4 N LYS B 14 ? N LYS B 28 O ASN B 13 ? O ASN B 27 # _database_PDB_matrix.entry_id 5AEF _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 # _atom_sites.entry_id 5AEF _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 # loop_ _atom_type.symbol C N O S # 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 GLN 1 15 15 GLN GLN A . n A 1 2 LYS 2 16 16 LYS LYS A . n A 1 3 LEU 3 17 17 LEU LEU A . n A 1 4 VAL 4 18 18 VAL VAL A . n A 1 5 PHE 5 19 19 PHE PHE A . n A 1 6 PHE 6 20 20 PHE PHE A . n A 1 7 ALA 7 21 21 ALA ALA A . n A 1 8 GLU 8 22 22 GLU GLU A . n A 1 9 ASP 9 23 23 ASP ASP A . n A 1 10 VAL 10 24 24 VAL VAL A . n A 1 11 GLY 11 25 25 GLY GLY A . n A 1 12 SER 12 26 26 SER SER A . n A 1 13 ASN 13 27 27 ASN ASN A . n A 1 14 LYS 14 28 28 LYS LYS A . n A 1 15 GLY 15 29 29 GLY GLY A . n A 1 16 ALA 16 30 30 ALA ALA A . n A 1 17 ILE 17 31 31 ILE ILE A . n A 1 18 ILE 18 32 32 ILE ILE A . n A 1 19 GLY 19 33 33 GLY GLY A . n A 1 20 LEU 20 34 34 LEU LEU A . n A 1 21 MET 21 35 35 MET MET A . n A 1 22 VAL 22 36 36 VAL VAL A . n A 1 23 GLY 23 37 37 GLY GLY A . n A 1 24 GLY 24 38 38 GLY GLY A . n A 1 25 VAL 25 39 39 VAL VAL A . n A 1 26 VAL 26 40 40 VAL VAL A . n A 1 27 ILE 27 41 41 ILE ILE A . n A 1 28 ALA 28 42 42 ALA ALA A . n B 1 1 GLN 1 15 15 GLN GLN B . n B 1 2 LYS 2 16 16 LYS LYS B . n B 1 3 LEU 3 17 17 LEU LEU B . n B 1 4 VAL 4 18 18 VAL VAL B . n B 1 5 PHE 5 19 19 PHE PHE B . n B 1 6 PHE 6 20 20 PHE PHE B . n B 1 7 ALA 7 21 21 ALA ALA B . n B 1 8 GLU 8 22 22 GLU GLU B . n B 1 9 ASP 9 23 23 ASP ASP B . n B 1 10 VAL 10 24 24 VAL VAL B . n B 1 11 GLY 11 25 25 GLY GLY B . n B 1 12 SER 12 26 26 SER SER B . n B 1 13 ASN 13 27 27 ASN ASN B . n B 1 14 LYS 14 28 28 LYS LYS B . n B 1 15 GLY 15 29 29 GLY GLY B . n B 1 16 ALA 16 30 30 ALA ALA B . n B 1 17 ILE 17 31 31 ILE ILE B . n B 1 18 ILE 18 32 32 ILE ILE B . n B 1 19 GLY 19 33 33 GLY GLY B . n B 1 20 LEU 20 34 34 LEU LEU B . n B 1 21 MET 21 35 35 MET MET B . n B 1 22 VAL 22 36 36 VAL VAL B . n B 1 23 GLY 23 37 37 GLY GLY B . n B 1 24 GLY 24 38 38 GLY GLY B . n B 1 25 VAL 25 39 39 VAL VAL B . n B 1 26 VAL 26 40 40 VAL VAL B . n B 1 27 ILE 27 41 41 ILE ILE B . n B 1 28 ALA 28 42 42 ALA ALA B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 # 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 2015-10-14 2 'Structure model' 1 1 2015-10-21 3 'Structure model' 1 2 2017-08-30 4 'Structure model' 1 3 2018-10-03 5 'Structure model' 1 4 2019-10-02 6 'Structure model' 1 5 2019-10-23 # _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_ _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' 'Database references' 2 3 'Structure model' Advisory 3 4 'Structure model' 'Data collection' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' Other 6 6 'Structure model' 'Data collection' 7 6 'Structure model' Other # 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 3 'Structure model' pdbx_validate_polymer_linkage 2 4 'Structure model' em_software 3 5 'Structure model' atom_sites 4 5 'Structure model' cell 5 6 'Structure model' cell # 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 3 'Structure model' '_pdbx_validate_polymer_linkage.dist' 2 3 'Structure model' '_pdbx_validate_polymer_linkage.label_alt_id_1' 3 3 'Structure model' '_pdbx_validate_polymer_linkage.label_alt_id_2' 4 4 'Structure model' '_em_software.image_processing_id' 5 5 'Structure model' '_atom_sites.fract_transf_matrix[1][1]' 6 5 'Structure model' '_atom_sites.fract_transf_matrix[2][2]' 7 5 'Structure model' '_atom_sites.fract_transf_matrix[3][3]' 8 5 'Structure model' '_cell.length_a' 9 5 'Structure model' '_cell.length_b' 10 5 'Structure model' '_cell.length_c' 11 6 'Structure model' '_cell.Z_PDB' # _pdbx_database_remark.id 700 _pdbx_database_remark.text ; SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 3-STRANDED BARREL THIS IS REPRESENTED BY A 4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. ; # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 5AEF _em_3d_fitting.ref_protocol OTHER _em_3d_fitting.ref_space REAL _em_3d_fitting.overall_b_value ? _em_3d_fitting.target_criteria 'ELECTRON DENSITY' _em_3d_fitting.details 'METHOD--DIREX REFINEMENT PROTOCOL--PEPTIDE CHAIN' _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 5AEF _em_3d_reconstruction.id 1 _em_3d_reconstruction.symmetry_type HELICAL _em_3d_reconstruction.num_particles 62320 _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.method 'PROJECTION MATCHING AND FOURIER INVERSION' _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size 1.2 _em_3d_reconstruction.resolution 5 _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.details ;FINAL MAP WAS CALCULATED FROM 29 SINGLE FILAMENT RECONSTRUCTIONS. DATA USED FOR REFINEMENT WAS NEVER BELOW 10 ANGSTROM RESOLUTION. RESOLUTION OF FIBRIL CORE IS ABOUT 5 ANGSTROM. 3 POSSIBLE MODELS FOR THE CENTRAL REGION OF A ABETA(1-42) FIBRIL RECONSTRUCTION. MODEL1 ABETA(17-42) MODEL2 ABETA( 16-41) MODEL3 ABETA(15-40) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3132. (DEPOSITION ID: 13698). ; _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.resolution_method ? _em_3d_reconstruction.algorithm ? # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name '50MM TRIS-HCL' _em_buffer.pH 7.4 _em_buffer.details '50MM TRIS-HCL' # _em_entity_assembly.id 1 _em_entity_assembly.name 'ABETA(1-42) AMYLOID-LIKE FIBRIL' _em_entity_assembly.type COMPLEX _em_entity_assembly.parent_id 0 _em_entity_assembly.synonym ? _em_entity_assembly.details FIBRIL _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 5AEF _em_image_scans.id 1 _em_image_scans.image_recording_id 1 _em_image_scans.number_digital_images 29 _em_image_scans.citation_id ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.details ? # _em_imaging.entry_id 5AEF _em_imaging.id 1 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.specimen_id 1 _em_imaging.date 2010-02-05 _em_imaging.temperature 100 _em_imaging.microscope_model 'FEI TECNAI F30' _em_imaging.nominal_defocus_min 1750 _em_imaging.nominal_defocus_max 3000 _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_cs 2.0 _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_magnification 59000 _em_imaging.calibrated_magnification 58333 _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.accelerating_voltage 300 _em_imaging.details ? _em_imaging.specimen_holder_type . _em_imaging.specimen_holder_model . _em_imaging.citation_id ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details 'HOLEY CARBON' _em_sample_support.method ? _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? # _em_vitrification.entry_id 5AEF _em_vitrification.id 1 _em_vitrification.instrument 'GATAN CRYOPLUNGE 3' _em_vitrification.cryogen_name ETHANE _em_vitrification.specimen_id 1 _em_vitrification.details '4 SEC BACKSIDE BLOTTING' _em_vitrification.citation_id ? _em_vitrification.humidity ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 5AEF _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method HELICAL # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 C A GLN 15 ? ? N A LEU 17 ? B 0.59 2 1 C B GLN 15 ? ? CD1 B LEU 17 ? C 0.64 3 1 O A VAL 39 ? A C A ALA 42 ? ? 0.67 4 1 C A VAL 39 ? A C A ALA 42 ? ? 0.79 5 1 C B GLN 15 ? ? N B LEU 17 ? B 0.80 6 1 CG2 B ILE 41 ? A CB B ALA 42 ? ? 0.83 7 1 N A VAL 39 ? A N A ALA 42 ? ? 0.98 8 1 CG2 B ILE 41 ? A CA B ALA 42 ? ? 1.03 9 1 O A VAL 39 ? A CA A ALA 42 ? ? 1.03 10 1 O B GLN 15 ? ? CD1 B LEU 17 ? C 1.12 11 1 CA B GLN 15 ? ? CD1 B LEU 17 ? C 1.31 12 1 CB B GLN 15 ? ? CD2 B LEU 17 ? C 1.33 13 1 C B GLN 15 ? ? C B LYS 16 ? B 1.35 14 1 O B GLN 15 ? ? N B LEU 17 ? B 1.38 15 1 C A GLN 15 ? ? C A LYS 16 ? B 1.41 16 1 CA A VAL 39 ? A N A ALA 42 ? ? 1.44 17 1 O A GLN 15 ? ? N A LEU 17 ? B 1.45 18 1 C A GLN 15 ? ? CA A LEU 17 ? B 1.60 19 1 CB B GLN 15 ? ? CG B LEU 17 ? C 1.64 20 1 N A VAL 40 ? A C A ALA 42 ? ? 1.67 21 1 C B GLN 15 ? ? CG B LEU 17 ? C 1.68 22 1 C A VAL 39 ? A CA A ALA 42 ? ? 1.70 23 1 CG1 B ILE 41 ? A N B ALA 42 ? ? 1.73 24 1 CB A GLN 15 ? ? CB A LEU 17 ? B 1.83 25 1 CA B GLN 15 ? ? CG B LEU 17 ? C 1.92 26 1 C B GLN 15 ? ? CA B LEU 17 ? B 1.94 27 1 CB A VAL 39 ? A N A ALA 42 ? ? 1.97 28 1 O A VAL 39 ? A CB A ALA 42 ? ? 2.00 29 1 CA A GLN 15 ? ? N A LEU 17 ? B 2.03 30 1 CB B GLN 15 ? ? CD1 B LEU 17 ? C 2.08 31 1 CB B GLN 15 ? ? CB B LEU 17 ? B 2.10 32 1 N B GLN 15 ? ? CD1 B LEU 17 ? C 2.16 33 1 CA A VAL 39 ? A CA A ALA 42 ? ? 2.16 34 1 C A GLN 15 ? ? CB A LEU 17 ? B 2.17 35 1 C A VAL 39 ? A N A ALA 42 ? ? 2.17 36 1 N A VAL 39 ? A CA A ALA 42 ? ? 2.18 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C A ILE 41 ? A O A ILE 41 ? ? 7.341 1.229 6.112 0.019 N 2 1 C B ILE 41 ? A O B ILE 41 ? ? 4.181 1.229 2.952 0.019 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CA A ILE 41 ? A C A ILE 41 ? A O A ILE 41 ? ? 49.31 120.10 -70.79 2.10 N 2 1 CA B ILE 41 ? A C B ILE 41 ? A O B ILE 41 ? ? 31.80 120.10 -88.30 2.10 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PHE A 20 ? A -116.54 53.81 2 1 LYS A 28 ? B -156.59 89.34 3 1 VAL A 36 ? A 80.71 111.69 4 1 LYS B 28 ? B -174.89 117.87 5 1 ALA B 30 ? A -99.17 54.44 6 1 VAL B 36 ? A 67.08 116.96 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 SER _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 26 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 A _pdbx_validate_peptide_omega.auth_comp_id_2 ASN _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 27 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 A _pdbx_validate_peptide_omega.omega -149.52 # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 C A GLN 15 ? ? N A LYS 16 ? B 3.43 2 1 C A VAL 40 ? B N A ILE 41 ? B 4.68 3 1 C A VAL 40 ? A N A ILE 41 ? A 7.99 4 1 C A ILE 41 ? A N A ALA 42 ? ? 5.78 5 1 C B GLN 15 ? ? N B LYS 16 ? B 3.14 6 1 C B VAL 40 ? B N B ILE 41 ? B 2.90 7 1 C B VAL 40 ? A N B ILE 41 ? A 7.66 8 1 C B ILE 41 ? A N B ALA 42 ? ? 3.60 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ILE 31 ? CD1 ? A ILE 17 CD1 2 1 Y 1 A ILE 32 ? CD1 ? A ILE 18 CD1 3 1 Y 1 A ILE 41 ? CD1 ? A ILE 27 CD1 4 1 Y 1 A ALA 42 ? O ? A ALA 28 O 5 1 Y 1 B ILE 31 ? CD1 ? B ILE 17 CD1 6 1 Y 1 B ILE 32 ? CD1 ? B ILE 18 CD1 7 1 Y 1 B ILE 41 ? CD1 ? B ILE 27 CD1 8 1 Y 1 B ALA 42 ? O ? B ALA 28 O # _em_ctf_correction.id 1 _em_ctf_correction.details 'INDIVIDUAL HELICAL SUBUNITS' _em_ctf_correction.type ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.avg_electron_dose_per_image 30 _em_image_recording.details ? _em_image_recording.id 1 _em_image_recording.film_or_detector_model 'KODAK SO-163 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 ? # _em_software.id 1 _em_software.name FREALIX _em_software.version ? _em_software.category RECONSTRUCTION _em_software.details ? _em_software.image_processing_id 1 _em_software.imaging_id ? _em_software.fitting_id ? # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration 1 _em_specimen.vitrification_applied YES _em_specimen.staining_applied NO _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details ? #