data_9A1A _entry.id 9A1A _struct.entry_id 9A1A _struct.title 'The ensemble structure of alpha-synuclein monomer' _struct.pdbx_structure_determination_methodology integrative # # 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 1.26 https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_flr_ext.dic mmcif_ihm_flr_ext.dic 0.01 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.395 # # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB-Dev PDBDEV_00000082 PDBDEV_00000082 ? PDB 9A1A pdb_00009a1a 10.2210/pdb9a1a/pdb # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A1A _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2021-03-10 # # 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 2021-05-06 # # _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_ _software.pdbx_ordinal _software.name _software.classification _software.description _software.version _software.type _software.location 1 piDMD 'model building' 'Discrete molecular dynamics simulations' . Program http://www.moleculesinaction.com/home.html 2 TTClust 'structure clustering' 'Software used for clustering' . Program https://github.com/tubiana/TTClust # # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI 1 'The structural heterogeneity of alpha-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds' Structure ? ? ? 2021 ? 10.1016/j.str.2021.05.002 2 'Segmental Conformational Disorder and Dynamics in the Intrinsically Disordered Protein alpha-Synuclein and Its Chain Length Dependence' 'J. Mol. Biol.' 405 1267 1283 2011 21108951 10.1016/j.jmb.2010.11.011 3 'Intramolecular dynamics of chain molecules monitored by fluctuations in efficiency of excitation energy transfer. A theoretical study' 'Biophys. J.' 46 429 437 1984 6498263 10.1016/S0006-3495(84)84040-0 # # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 'Chen J' 1 1 'Zaer S' 2 1 'Drori P' 3 1 'Zamel J' 4 1 'Joron K' 5 1 'Kalisman N' 6 1 'Lerner E' 7 1 'Dokholyan NV' 8 2 'Grupi A' 9 2 'Haas E' 10 3 'Haas E' 11 3 'Steinberg I Z' 12 # # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Chen J' 1 'Zaer S' 2 'Drori P' 3 'Zamel J' 4 'Joron K' 5 'Kalisman N' 6 'Lerner E' 7 'Dokholyan NV' 8 # # loop_ _chem_comp.id _chem_comp.type _chem_comp.name _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' ALANINE 'C3 H7 N O2' 89.094 ASN 'L-peptide linking' ASPARAGINE 'C4 H8 N2 O3' 132.119 ASP 'L-peptide linking' 'ASPARTIC ACID' 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' CYSTEINE 'C3 H7 N O2 S' 121.154 GLN 'L-peptide linking' GLUTAMINE 'C5 H10 N2 O3' 146.146 GLU 'L-peptide linking' 'GLUTAMIC ACID' 'C5 H9 N O4' 147.130 GLY 'peptide linking' GLYCINE 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' HISTIDINE 'C6 H10 N3 O2 1' 156.165 ILE 'L-peptide linking' ISOLEUCINE 'C6 H13 N O2' 131.175 LEU 'L-peptide linking' LEUCINE 'C6 H13 N O2' 131.175 LYS 'L-peptide linking' LYSINE 'C6 H15 N2 O2 1' 147.198 MET 'L-peptide linking' METHIONINE 'C5 H11 N O2 S' 149.208 PHE 'L-peptide linking' PHENYLALANINE 'C9 H11 N O2' 165.192 PRO 'L-peptide linking' PROLINE 'C5 H9 N O2' 115.132 SER 'L-peptide linking' SERINE 'C3 H7 N O3' 105.093 THR 'L-peptide linking' THREONINE 'C4 H9 N O3' 119.120 TRP 'L-peptide linking' TRYPTOPHAN 'C11 H12 N2 O2' 204.229 TYR 'L-peptide linking' TYROSINE 'C9 H11 N O3' 181.191 VAL 'L-peptide linking' VALINE 'C5 H11 N O2' 117.148 # # loop_ _ihm_chemical_component_descriptor.id _ihm_chemical_component_descriptor.auth_name _ihm_chemical_component_descriptor.chemical_name _ihm_chemical_component_descriptor.common_name _ihm_chemical_component_descriptor.smiles _ihm_chemical_component_descriptor.smiles_canonical _ihm_chemical_component_descriptor.inchi _ihm_chemical_component_descriptor.inchi_key 1 Tryptophan . . C1=CC=C2C(=C1)C(=CN2)CC(C(=O)O)N . . . 2 'Tryptophan chromophore' . . C1=CC=C2C(=C1)C(=CN2) . . . 3 '7-iodo-acetamidocoumarin- 4-carboxylic acid (I-Cou)' . . C1=CC2=C(C=C1NC(=O)CI)OC(=O)C=C2C(=O)O . . . 4 'Coumarin chromophore' . . C1=CC2=C(C=C1)OC(=O)C=C2 . . . 5 TryptophanConjugate . . C1=CC=C2C(=C1)C(=CN2)CC(C(=O)O)N . . . 6 I-Cou-Cys . . C1=C2C(=CC(=C1)NC(CSCC(C=O)N)=O)OC(C=C2C(=O)O)=O . . . # # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.details 1 polymer man 'alpha-synuclein' 16980.392 1 . # # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.details 1 1 UNP SYUA_HUMAN P37840 1 . . # # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end 1 1 1 140 1 140 # # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_strand_id _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can 1 polypeptide(L) no no A ;MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAV VTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA ; ;MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAV VTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA ; # # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET . 1 2 ASP . 1 3 VAL . 1 4 PHE . 1 5 MET . 1 6 LYS . 1 7 GLY . 1 8 LEU . 1 9 SER . 1 10 LYS . 1 11 ALA . 1 12 LYS . 1 13 GLU . 1 14 GLY . 1 15 VAL . 1 16 VAL . 1 17 ALA . 1 18 ALA . 1 19 ALA . 1 20 GLU . 1 21 LYS . 1 22 THR . 1 23 LYS . 1 24 GLN . 1 25 GLY . 1 26 VAL . 1 27 ALA . 1 28 GLU . 1 29 ALA . 1 30 ALA . 1 31 GLY . 1 32 LYS . 1 33 THR . 1 34 LYS . 1 35 GLU . 1 36 GLY . 1 37 VAL . 1 38 LEU . 1 39 TYR . 1 40 VAL . 1 41 GLY . 1 42 SER . 1 43 LYS . 1 44 THR . 1 45 LYS . 1 46 GLU . 1 47 GLY . 1 48 VAL . 1 49 VAL . 1 50 HIS . 1 51 GLY . 1 52 VAL . 1 53 ALA . 1 54 THR . 1 55 VAL . 1 56 ALA . 1 57 GLU . 1 58 LYS . 1 59 THR . 1 60 LYS . 1 61 GLU . 1 62 GLN . 1 63 VAL . 1 64 THR . 1 65 ASN . 1 66 VAL . 1 67 GLY . 1 68 GLY . 1 69 ALA . 1 70 VAL . 1 71 VAL . 1 72 THR . 1 73 GLY . 1 74 VAL . 1 75 THR . 1 76 ALA . 1 77 VAL . 1 78 ALA . 1 79 GLN . 1 80 LYS . 1 81 THR . 1 82 VAL . 1 83 GLU . 1 84 GLY . 1 85 ALA . 1 86 GLY . 1 87 SER . 1 88 ILE . 1 89 ALA . 1 90 ALA . 1 91 ALA . 1 92 THR . 1 93 GLY . 1 94 PHE . 1 95 VAL . 1 96 LYS . 1 97 LYS . 1 98 ASP . 1 99 GLN . 1 100 LEU . 1 101 GLY . 1 102 LYS . 1 103 ASN . 1 104 GLU . 1 105 GLU . 1 106 GLY . 1 107 ALA . 1 108 PRO . 1 109 GLN . 1 110 GLU . 1 111 GLY . 1 112 ILE . 1 113 LEU . 1 114 GLU . 1 115 ASP . 1 116 MET . 1 117 PRO . 1 118 VAL . 1 119 ASP . 1 120 PRO . 1 121 ASP . 1 122 ASN . 1 123 GLU . 1 124 ALA . 1 125 TYR . 1 126 GLU . 1 127 MET . 1 128 PRO . 1 129 SER . 1 130 GLU . 1 131 GLU . 1 132 GLY . 1 133 TYR . 1 134 GLN . 1 135 ASP . 1 136 TYR . 1 137 GLU . 1 138 PRO . 1 139 GLU . 1 140 ALA . # # loop_ _ihm_entity_poly_segment.id _ihm_entity_poly_segment.entity_id _ihm_entity_poly_segment.seq_id_begin _ihm_entity_poly_segment.seq_id_end _ihm_entity_poly_segment.comp_id_begin _ihm_entity_poly_segment.comp_id_end 1 1 1 140 MET ALA # # loop_ _struct_asym.id _struct_asym.entity_id _struct_asym.details A 1 . # # 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 A 1 1 MET 1 1 MET MET A A 1 2 ASP 2 2 ASP ASP A A 1 3 VAL 3 3 VAL VAL A A 1 4 PHE 4 4 PHE PHE A A 1 5 MET 5 5 MET MET A A 1 6 LYS 6 6 LYS LYS A A 1 7 GLY 7 7 GLY GLY A A 1 8 LEU 8 8 LEU LEU A A 1 9 SER 9 9 SER SER A A 1 10 LYS 10 10 LYS LYS A A 1 11 ALA 11 11 ALA ALA A A 1 12 LYS 12 12 LYS LYS A A 1 13 GLU 13 13 GLU GLU A A 1 14 GLY 14 14 GLY GLY A A 1 15 VAL 15 15 VAL VAL A A 1 16 VAL 16 16 VAL VAL A A 1 17 ALA 17 17 ALA ALA A A 1 18 ALA 18 18 ALA ALA A A 1 19 ALA 19 19 ALA ALA A A 1 20 GLU 20 20 GLU GLU A A 1 21 LYS 21 21 LYS LYS A A 1 22 THR 22 22 THR THR A A 1 23 LYS 23 23 LYS LYS A A 1 24 GLN 24 24 GLN GLN A A 1 25 GLY 25 25 GLY GLY A A 1 26 VAL 26 26 VAL VAL A A 1 27 ALA 27 27 ALA ALA A A 1 28 GLU 28 28 GLU GLU A A 1 29 ALA 29 29 ALA ALA A A 1 30 ALA 30 30 ALA ALA A A 1 31 GLY 31 31 GLY GLY A A 1 32 LYS 32 32 LYS LYS A A 1 33 THR 33 33 THR THR A A 1 34 LYS 34 34 LYS LYS A A 1 35 GLU 35 35 GLU GLU A A 1 36 GLY 36 36 GLY GLY A A 1 37 VAL 37 37 VAL VAL A A 1 38 LEU 38 38 LEU LEU A A 1 39 TYR 39 39 TYR TYR A A 1 40 VAL 40 40 VAL VAL A A 1 41 GLY 41 41 GLY GLY A A 1 42 SER 42 42 SER SER A A 1 43 LYS 43 43 LYS LYS A A 1 44 THR 44 44 THR THR A A 1 45 LYS 45 45 LYS LYS A A 1 46 GLU 46 46 GLU GLU A A 1 47 GLY 47 47 GLY GLY A A 1 48 VAL 48 48 VAL VAL A A 1 49 VAL 49 49 VAL VAL A A 1 50 HIS 50 50 HIS HIS A A 1 51 GLY 51 51 GLY GLY A A 1 52 VAL 52 52 VAL VAL A A 1 53 ALA 53 53 ALA ALA A A 1 54 THR 54 54 THR THR A A 1 55 VAL 55 55 VAL VAL A A 1 56 ALA 56 56 ALA ALA A A 1 57 GLU 57 57 GLU GLU A A 1 58 LYS 58 58 LYS LYS A A 1 59 THR 59 59 THR THR A A 1 60 LYS 60 60 LYS LYS A A 1 61 GLU 61 61 GLU GLU A A 1 62 GLN 62 62 GLN GLN A A 1 63 VAL 63 63 VAL VAL A A 1 64 THR 64 64 THR THR A A 1 65 ASN 65 65 ASN ASN A A 1 66 VAL 66 66 VAL VAL A A 1 67 GLY 67 67 GLY GLY A A 1 68 GLY 68 68 GLY GLY A A 1 69 ALA 69 69 ALA ALA A A 1 70 VAL 70 70 VAL VAL A A 1 71 VAL 71 71 VAL VAL A A 1 72 THR 72 72 THR THR A A 1 73 GLY 73 73 GLY GLY A A 1 74 VAL 74 74 VAL VAL A A 1 75 THR 75 75 THR THR A A 1 76 ALA 76 76 ALA ALA A A 1 77 VAL 77 77 VAL VAL A A 1 78 ALA 78 78 ALA ALA A A 1 79 GLN 79 79 GLN GLN A A 1 80 LYS 80 80 LYS LYS A A 1 81 THR 81 81 THR THR A A 1 82 VAL 82 82 VAL VAL A A 1 83 GLU 83 83 GLU GLU A A 1 84 GLY 84 84 GLY GLY A A 1 85 ALA 85 85 ALA ALA A A 1 86 GLY 86 86 GLY GLY A A 1 87 SER 87 87 SER SER A A 1 88 ILE 88 88 ILE ILE A A 1 89 ALA 89 89 ALA ALA A A 1 90 ALA 90 90 ALA ALA A A 1 91 ALA 91 91 ALA ALA A A 1 92 THR 92 92 THR THR A A 1 93 GLY 93 93 GLY GLY A A 1 94 PHE 94 94 PHE PHE A A 1 95 VAL 95 95 VAL VAL A A 1 96 LYS 96 96 LYS LYS A A 1 97 LYS 97 97 LYS LYS A A 1 98 ASP 98 98 ASP ASP A A 1 99 GLN 99 99 GLN GLN A A 1 100 LEU 100 100 LEU LEU A A 1 101 GLY 101 101 GLY GLY A A 1 102 LYS 102 102 LYS LYS A A 1 103 ASN 103 103 ASN ASN A A 1 104 GLU 104 104 GLU GLU A A 1 105 GLU 105 105 GLU GLU A A 1 106 GLY 106 106 GLY GLY A A 1 107 ALA 107 107 ALA ALA A A 1 108 PRO 108 108 PRO PRO A A 1 109 GLN 109 109 GLN GLN A A 1 110 GLU 110 110 GLU GLU A A 1 111 GLY 111 111 GLY GLY A A 1 112 ILE 112 112 ILE ILE A A 1 113 LEU 113 113 LEU LEU A A 1 114 GLU 114 114 GLU GLU A A 1 115 ASP 115 115 ASP ASP A A 1 116 MET 116 116 MET MET A A 1 117 PRO 117 117 PRO PRO A A 1 118 VAL 118 118 VAL VAL A A 1 119 ASP 119 119 ASP ASP A A 1 120 PRO 120 120 PRO PRO A A 1 121 ASP 121 121 ASP ASP A A 1 122 ASN 122 122 ASN ASN A A 1 123 GLU 123 123 GLU GLU A A 1 124 ALA 124 124 ALA ALA A A 1 125 TYR 125 125 TYR TYR A A 1 126 GLU 126 126 GLU GLU A A 1 127 MET 127 127 MET MET A A 1 128 PRO 128 128 PRO PRO A A 1 129 SER 129 129 SER SER A A 1 130 GLU 130 130 GLU GLU A A 1 131 GLU 131 131 GLU GLU A A 1 132 GLY 132 132 GLY GLY A A 1 133 TYR 133 133 TYR TYR A A 1 134 GLN 134 134 GLN GLN A A 1 135 ASP 135 135 ASP ASP A A 1 136 TYR 136 136 TYR TYR A A 1 137 GLU 137 137 GLU GLU A A 1 138 PRO 138 138 PRO PRO A A 1 139 GLU 139 139 GLU GLU A A 1 140 ALA 140 140 ALA ALA A # # loop_ _ihm_struct_assembly.id _ihm_struct_assembly.name _ihm_struct_assembly.description 1 'Complete assembly' ; The ensemble structure of alpha-synuclein monomer determined using FRET data and discrete molecular dynamics simulations. ; # # loop_ _ihm_struct_assembly_details.id _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.parent_assembly_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_poly_segment_id 1 1 1 'alpha-synuclein' 1 A 1 # # loop_ _ihm_external_reference_info.reference_id _ihm_external_reference_info.reference_provider _ihm_external_reference_info.reference_type _ihm_external_reference_info.reference _ihm_external_reference_info.refers_to _ihm_external_reference_info.associated_url _ihm_external_reference_info.details 1 Zenodo DOI 10.5281/zenodo.4721617 Other https://zenodo.org/record/4721617 'Zenodo record consists of 8 individual PDB files comprising of 8 structural ensembles representing each output cluster' 2 . DOI 10.1016/j.jmb.2010.11.011 File https://www.sciencedirect.com/science/article/abs/pii/S0022283610012258 . # # loop_ _ihm_external_files.id _ihm_external_files.reference_id _ihm_external_files.file_path _ihm_external_files.content_type _ihm_external_files.file_size_bytes _ihm_external_files.details 1 1 'Cluster1.pdb' 'Modeling or post-processing output' . . 2 1 'Cluster2.pdb' 'Modeling or post-processing output' . . 3 1 'Cluster3.pdb' 'Modeling or post-processing output' . . 4 1 'Cluster4.pdb' 'Modeling or post-processing output' . . 5 1 'Cluster5.pdb' 'Modeling or post-processing output' . . 6 1 'Cluster6.pdb' 'Modeling or post-processing output' . . 7 1 'Cluster7.pdb' 'Modeling or post-processing output' . . 8 1 'Cluster8.pdb' 'Modeling or post-processing output' . . 9 2 . 'Input data or restraints' . 'FRET restraints obtained from publication' # # loop_ _ihm_dataset_list.id _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details 1 'Other' NO 'Restraints from time-resolved ensemble FRET' # # loop_ _ihm_dataset_group.id _ihm_dataset_group.name _ihm_dataset_group.application _ihm_dataset_group.details 1 . . . # # loop_ _ihm_dataset_group_link.group_id _ihm_dataset_group_link.dataset_list_id 1 1 # # loop_ _ihm_dataset_external_reference.id _ihm_dataset_external_reference.dataset_list_id _ihm_dataset_external_reference.file_id 1 1 9 # # loop_ _ihm_model_representation.id _ihm_model_representation.name _ihm_model_representation.details 1 . . # # loop_ _ihm_model_representation_details.id _ihm_model_representation_details.representation_id _ihm_model_representation_details.entity_id _ihm_model_representation_details.entity_description _ihm_model_representation_details.entity_asym_id _ihm_model_representation_details.entity_poly_segment_id _ihm_model_representation_details.model_object_primitive _ihm_model_representation_details.starting_model_id _ihm_model_representation_details.model_mode _ihm_model_representation_details.model_granularity _ihm_model_representation_details.model_object_count _ihm_model_representation_details.description 1 1 1 'alpha-synuclein' A 1 atomistic . flexible by-atom . . # # loop_ _ihm_modeling_protocol.id _ihm_modeling_protocol.protocol_name _ihm_modeling_protocol.num_steps 1 'Modeling using FRET restraints' 1 # # loop_ _ihm_modeling_protocol_details.id _ihm_modeling_protocol_details.protocol_id _ihm_modeling_protocol_details.step_id _ihm_modeling_protocol_details.struct_assembly_id _ihm_modeling_protocol_details.dataset_group_id _ihm_modeling_protocol_details.struct_assembly_description _ihm_modeling_protocol_details.step_name _ihm_modeling_protocol_details.step_method _ihm_modeling_protocol_details.num_models_begin _ihm_modeling_protocol_details.num_models_end _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag _ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.description 1 1 1 1 1 'alpha-synuclein monomer' 'Discrete molecular dynamics simulations' . 0 30303 NO NO NO YES 1 . . # # loop_ _ihm_modeling_post_process.id _ihm_modeling_post_process.protocol_id _ihm_modeling_post_process.analysis_id _ihm_modeling_post_process.step_id _ihm_modeling_post_process.type _ihm_modeling_post_process.feature _ihm_modeling_post_process.num_models_begin _ihm_modeling_post_process.num_models_end _ihm_modeling_post_process.struct_assembly_id _ihm_modeling_post_process.dataset_group_id _ihm_modeling_post_process.software_id _ihm_modeling_post_process.script_file_id _ihm_modeling_post_process.details 1 1 1 1 cluster RMSD . . 1 1 2 . . # # loop_ _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.assembly_id _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 cluster1_centroid 1 1 1 2 cluster2_centroid 1 1 1 3 cluster3_centroid 1 1 1 4 cluster4_centroid 1 1 1 5 cluster5_centroid 1 1 1 6 cluster6_centroid 1 1 1 7 cluster7_centroid 1 1 1 8 cluster8_centroid 1 1 1 # # loop_ _ihm_model_group.id _ihm_model_group.name _ihm_model_group.details 1 'cluster 1' . 2 'cluster 2' . 3 'cluster 3' . 4 'cluster 4' . 5 'cluster 5' . 6 'cluster 6' . 7 'cluster 7' . 8 'cluster 8' . # # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 # # loop_ # # loop_ _atom_type.symbol C H N O S # # loop_ _ihm_ensemble_info.ensemble_id _ihm_ensemble_info.ensemble_name _ihm_ensemble_info.post_process_id _ihm_ensemble_info.model_group_id _ihm_ensemble_info.ensemble_clustering_method _ihm_ensemble_info.ensemble_clustering_feature _ihm_ensemble_info.num_ensemble_models _ihm_ensemble_info.num_ensemble_models_deposited _ihm_ensemble_info.ensemble_precision_value _ihm_ensemble_info.ensemble_file_id _ihm_ensemble_info.details _ihm_ensemble_info.sub_sample_flag _ihm_ensemble_info.sub_sampling_type 1 'Cluster 1 ensemble of alpha-synuclein monomer' 1 1 Hierarchical RMSD . 1 . 1 . NO . 2 'Cluster 2 ensemble of alpha-synuclein monomer' 1 2 Hierarchical RMSD . 1 . 2 . NO . 3 'Cluster 3 ensemble of alpha-synuclein monomer' 1 3 Hierarchical RMSD . 1 . 3 . NO . 4 'Cluster 4 ensemble of alpha-synuclein monomer' 1 4 Hierarchical RMSD . 1 . 4 . NO . 5 'Cluster 5 ensemble of alpha-synuclein monomer' 1 5 Hierarchical RMSD . 1 . 5 . NO . 6 'Cluster 6 ensemble of alpha-synuclein monomer' 1 6 Hierarchical RMSD . 1 . 6 . NO . 7 'Cluster 7 ensemble of alpha-synuclein monomer' 1 7 Hierarchical RMSD . 1 . 7 . NO . 8 'Cluster 8 ensemble of alpha-synuclein monomer' 1 8 Hierarchical RMSD . 1 . 8 . NO . # # loop_ _flr_experiment.ordinal_id _flr_experiment.id _flr_experiment.instrument_id _flr_experiment.inst_setting_id _flr_experiment.exp_condition_id _flr_experiment.sample_id _flr_experiment.details 1 1 1 1 1 1 . 2 1 1 1 1 2 . 3 1 1 1 1 3 . 4 1 1 1 1 4 . 5 1 1 1 1 5 . 6 1 1 1 1 6 . 7 1 1 1 1 7 . 8 1 1 1 1 8 . # # loop_ _flr_inst_setting.id _flr_inst_setting.details 1 ;Samples were excited at 297 nm (pulse FWHM of 60 ps), and the fluorescence emission was collected through a polarizer oriented at the “magic angle” (55°) relative to the polarization of the 297 nm excitation beam. Average data collection time was 5-15 min. Background emission of a buffer solution was recorded for 5 min and subtracted from the protein sample decay. ; # # loop_ _flr_exp_condition.id _flr_exp_condition.details 1 'Samples were measured under 20 °C.' # # loop_ _flr_instrument.id _flr_instrument.details 1 'Aviv model ATF 105 spectrofluorometer (Aviv, USA)' # # loop_ _flr_entity_assembly.ordinal_id _flr_entity_assembly.assembly_id _flr_entity_assembly.entity_id _flr_entity_assembly.num_copies _flr_entity_assembly.entity_description 1 1 1 8 'alpha-synuclein' # # loop_ _flr_sample_condition.id _flr_sample_condition.details 1 '10-20 µM (800 µl) protein in filtered (0.22 µm) 20 mM Tris, 2 mM EDTA (pH 7.5). ' 2 . # # loop_ _flr_sample.id _flr_sample.entity_assembly_id _flr_sample.num_of_probes _flr_sample.sample_condition_id _flr_sample.sample_description _flr_sample.sample_details _flr_sample.solvent_phase 1 1 2 1 'alpha-synuclein monomer1' . liquid 2 1 2 1 'alpha-synuclein monomer2' . liquid 3 1 2 1 'alpha-synuclein monomer3' . liquid 4 1 2 1 'alpha-synuclein monomer4' . liquid 5 1 2 1 'alpha-synuclein monomer5' . liquid 6 1 2 1 'alpha-synuclein monomer6' . liquid 7 1 2 1 'alpha-synuclein monomer7' . liquid 8 1 2 1 'alpha-synuclein monomer8' . liquid 9 1 1 2 'alpha-synuclein donor-only' . liquid # # loop_ _flr_probe_list.probe_id _flr_probe_list.chromophore_name _flr_probe_list.reactive_probe_flag _flr_probe_list.reactive_probe_name _flr_probe_list.probe_origin _flr_probe_list.probe_link_type 1 Tryptophan YES Tryptophan extrinsic covalent 2 '7-iodo-acetamidocoumarin- 4-carboxylic acid (I-Cou)' YES '7-iodo-acetamidocoumarin- 4-carboxylic acid (I-Cou)' extrinsic covalent # # loop_ _flr_probe_descriptor.probe_id _flr_probe_descriptor.reactive_probe_chem_descriptor_id _flr_probe_descriptor.chromophore_chem_descriptor_id _flr_probe_descriptor.chromophore_center_atom 1 1 2 C 2 3 4 C # # loop_ _flr_sample_probe_details.sample_probe_id _flr_sample_probe_details.sample_id _flr_sample_probe_details.probe_id _flr_sample_probe_details.fluorophore_type _flr_sample_probe_details.description _flr_sample_probe_details.poly_probe_position_id 1 1 1 donor 'Donor in (D)A_V26W_(A)A_A18C' 1 2 1 2 acceptor 'Acceptor in (D)A_V26W_(A)A_A18C' 2 3 2 1 donor 'Donor in (D)A_Y39W_(A)A_V26C' 3 4 2 2 acceptor 'Acceptor in (D)A_Y39W_(A)A_V26C' 4 5 3 1 donor 'Donor in (D)A_F4W_(A)A_A18C' 5 6 3 2 acceptor 'Acceptor in (D)A_F4W_(A)A_A18C' 2 7 4 1 donor 'Donor in (D)A_Y39W_(A)A_A18C' 3 8 4 2 acceptor 'Acceptor in (D)A_Y39W_(A)A_A18C' 2 9 5 1 donor 'Donor in (D)A_F4W_(A)A_V26C' 5 10 5 2 acceptor 'Acceptor in (D)A_F4W_(A)A_V26C' 4 11 6 1 donor 'Donor in (D)A_A90W_(A)A_V66C' 6 12 6 2 acceptor 'Acceptor in (D)A_A90W_(A)A_V66C' 7 13 7 1 donor 'Donor in (D)A_Y39W_(A)A_V66C' 3 14 7 2 acceptor 'Acceptor in (D)A_Y39W_(A)A_V66C' 7 15 8 1 donor 'Donor in (D)A_Y39W_(A)A_F4C' 3 16 8 2 acceptor 'Acceptor in (D)A_Y39W_(A)A_F4C' 8 17 9 1 donor Donor-only 1 18 9 1 donor Donor-only 3 19 9 1 donor Donor-only 5 20 9 1 donor Donor-only 6 # # loop_ _flr_poly_probe_position.id _flr_poly_probe_position.entity_id _flr_poly_probe_position.entity_description _flr_poly_probe_position.asym_id _flr_poly_probe_position.seq_id _flr_poly_probe_position.comp_id _flr_poly_probe_position.atom_id _flr_poly_probe_position.mutation_flag _flr_poly_probe_position.modification_flag _flr_poly_probe_position.auth_name 1 1 'alpha-synuclein' A 26 VAL CA YES NO (D)A_V26W 2 1 'alpha-synuclein' A 18 ALA SG YES NO (A)A_A18C 3 1 'alpha-synuclein' A 39 TYR CA YES NO (D)A_Y39W 4 1 'alpha-synuclein' A 26 VAL SG YES NO (A)A_V26C 5 1 'alpha-synuclein' A 4 PHE CA YES NO (D)A_F4W 6 1 'alpha-synuclein' A 90 ALA CA YES NO (D)A_A90W 7 1 'alpha-synuclein' A 66 VAL SG YES NO (A)A_V66C 8 1 'alpha-synuclein' A 4 PHE SG YES NO (A)A_F4C # # loop_ _flr_poly_probe_position_mutated.id _flr_poly_probe_position_mutated.chem_comp_id _flr_poly_probe_position_mutated.atom_id 1 TRP CA 2 CYS SG 3 TRP CA 4 CYS SG 5 TRP CA 6 TRP CA 7 CYS SG 8 CYS SG # # loop_ _flr_poly_probe_conjugate.id _flr_poly_probe_conjugate.sample_probe_id _flr_poly_probe_conjugate.chem_descriptor_id _flr_poly_probe_conjugate.ambiguous_stoichiometry_flag _flr_poly_probe_conjugate.probe_stoichiometry 1 17 5 NO . 2 18 5 NO . 3 19 5 NO . 4 20 5 NO . 5 1 1 NO . 6 3 1 NO . 7 5 1 NO . 8 7 1 NO . 9 9 1 NO . 10 11 1 NO . 11 13 1 NO . 12 15 1 NO . 13 2 6 NO . 14 4 6 NO . 15 6 6 NO . 16 8 6 NO . 17 10 6 NO . 18 12 6 NO . 19 14 6 NO . 20 16 6 NO . # # loop_ _flr_fret_forster_radius.id _flr_fret_forster_radius.donor_probe_id _flr_fret_forster_radius.acceptor_probe_id _flr_fret_forster_radius.forster_radius _flr_fret_forster_radius.reduced_forster_radius 1 1 2 24.000 . # # loop_ _flr_lifetime_fit_model.id _flr_lifetime_fit_model.name _flr_lifetime_fit_model.description _flr_lifetime_fit_model.external_file_id _flr_lifetime_fit_model.citation_id 1 'The Haas-Steinberg model of a FRET-based distance distribution, with diffusion-enhancement' . . 3 # # loop_ _flr_reference_measurement_group.id _flr_reference_measurement_group.num_measurements _flr_reference_measurement_group.details 1 1 . 2 1 . 3 1 . 4 1 . # # loop_ _flr_reference_measurement_group_link.group_id _flr_reference_measurement_group_link.reference_measurement_id 1 1 2 2 3 3 4 4 # # loop_ _flr_reference_measurement.id _flr_reference_measurement.reference_sample_probe_id _flr_reference_measurement.num_species _flr_reference_measurement.details 1 17 3 . 2 18 3 . 3 19 3 . 4 20 3 . # # loop_ _flr_reference_measurement_lifetime.ordinal_id _flr_reference_measurement_lifetime.reference_measurement_id _flr_reference_measurement_lifetime.species_name _flr_reference_measurement_lifetime.species_fraction _flr_reference_measurement_lifetime.lifetime 1 1 Tryptophan 0.300 4.000 2 1 Tryptophan 0.440 1.800 3 1 Tryptophan 0.260 0.400 4 2 Tryptophan 0.410 4.000 5 2 Tryptophan 0.370 1.700 6 2 Tryptophan 0.220 0.400 7 3 Tryptophan 0.470 4.000 8 3 Tryptophan 0.350 1.600 9 3 Tryptophan 0.180 0.400 10 4 Tryptophan 0.520 3.800 11 4 Tryptophan 0.320 1.600 12 4 Tryptophan 0.160 0.400 # # loop_ _flr_fret_analysis.id _flr_fret_analysis.experiment_id _flr_fret_analysis.type _flr_fret_analysis.sample_probe_id_1 _flr_fret_analysis.sample_probe_id_2 _flr_fret_analysis.forster_radius_id _flr_fret_analysis.dataset_list_id _flr_fret_analysis.external_file_id _flr_fret_analysis.software_id 1 1 lifetime-based 1 2 1 1 . . 2 1 lifetime-based 3 4 1 1 . . 3 1 lifetime-based 5 6 1 1 . . 4 1 lifetime-based 7 8 1 1 . . 5 1 lifetime-based 9 10 1 1 . . 6 1 lifetime-based 11 12 1 1 . . 7 1 lifetime-based 13 14 1 1 . . 8 1 lifetime-based 15 16 1 1 . . # # loop_ _flr_fret_analysis_lifetime.ordinal_id _flr_fret_analysis_lifetime.analysis_id _flr_fret_analysis_lifetime.reference_measurement_group_id _flr_fret_analysis_lifetime.lifetime_fit_model_id _flr_fret_analysis_lifetime.donor_only_fraction _flr_fret_analysis_lifetime.chi_square_reduced _flr_fret_analysis_lifetime.method_name _flr_fret_analysis_lifetime.details 1 1 1 1 . 1.800 'the best-fit skewed Gaussian distance distribution was retrieved' . 2 2 2 1 . 1.900 'the best-fit skewed Gaussian distance distribution was retrieved' . 3 3 3 1 . 1.100 'the best-fit skewed Gaussian distance distribution was retrieved' . 4 4 2 1 . 1.200 'the best-fit skewed Gaussian distance distribution was retrieved' . 5 5 3 1 . 1.200 'the best-fit skewed Gaussian distance distribution was retrieved' . 6 6 4 1 . 1.400 'the best-fit skewed Gaussian distance distribution was retrieved' . 7 7 2 1 . 1.100 'the best-fit skewed Gaussian distance distribution was retrieved' . 8 8 2 1 . 1.200 'the best-fit skewed Gaussian distance distribution was retrieved' . # # loop_ _flr_peak_assignment.id _flr_peak_assignment.method_name _flr_peak_assignment.details 1 . . # # loop_ _flr_fret_distance_restraint.ordinal_id _flr_fret_distance_restraint.id _flr_fret_distance_restraint.group_id _flr_fret_distance_restraint.sample_probe_id_1 _flr_fret_distance_restraint.sample_probe_id_2 _flr_fret_distance_restraint.state_id _flr_fret_distance_restraint.analysis_id _flr_fret_distance_restraint.distance _flr_fret_distance_restraint.distance_error_plus _flr_fret_distance_restraint.distance_error_minus _flr_fret_distance_restraint.distance_type _flr_fret_distance_restraint.population_fraction _flr_fret_distance_restraint.peak_assignment_id 1 1 1 1 2 . 1 15.100 . . . 1.000 1 2 2 1 3 4 . 2 21.800 . . . 1.000 1 3 3 1 5 6 . 3 24.600 . . . 1.000 1 4 4 1 7 8 . 4 29.400 . . . 1.000 1 5 5 1 9 10 . 5 33.600 . . . 1.000 1 6 6 1 11 12 . 6 33.800 . . . 1.000 1 7 7 1 13 14 . 7 40.100 . . . 1.000 1 8 8 1 15 16 . 8 43.000 . . . 1.000 1 # # loop_ _flr_fret_model_distance.id _flr_fret_model_distance.restraint_id _flr_fret_model_distance.model_id _flr_fret_model_distance.distance _flr_fret_model_distance.distance_deviation 1 1 1 14.300 0.800 2 2 1 16.500 5.300 3 3 1 33.700 -9.100 4 4 1 20.500 8.900 5 5 1 44.700 -11.100 6 6 1 30.900 2.900 7 7 1 46.700 -6.600 8 8 1 52.000 -9.000 9 1 2 17.300 -2.200 10 2 2 16.800 5.000 11 3 2 23.300 1.300 12 4 2 24.000 5.400 13 5 2 27.200 6.400 14 6 2 27.000 6.800 15 7 2 31.500 8.600 16 8 2 41.100 1.900 17 1 3 10.100 5.000 18 2 3 26.700 -4.900 19 3 3 31.000 -6.400 20 4 3 30.300 -0.900 21 5 3 29.500 4.100 22 6 3 29.600 4.200 23 7 3 43.000 -2.900 24 8 3 7.700 35.300 25 1 4 22.800 -7.700 26 2 4 20.100 1.700 27 3 4 13.000 11.600 28 4 4 38.400 -9.000 29 5 4 31.700 1.900 30 6 4 33.500 0.300 31 7 4 33.000 7.100 32 8 4 47.200 -4.200 33 1 5 6.800 8.300 34 2 5 14.500 7.300 35 3 5 20.900 3.700 36 4 5 20.800 8.600 37 5 5 24.200 9.400 38 6 5 13.500 20.300 39 7 5 36.300 3.800 40 8 5 36.500 6.500 41 1 6 12.200 2.900 42 2 6 18.900 2.900 43 3 6 20.100 4.500 44 4 6 20.000 9.400 45 5 6 20.500 13.100 46 6 6 20.400 13.400 47 7 6 24.200 15.900 48 8 6 36.000 7.000 49 1 7 11.100 4.000 50 2 7 9.400 12.400 51 3 7 10.300 14.300 52 4 7 18.600 10.800 53 5 7 19.600 14.000 54 6 7 30.000 3.800 55 7 7 17.900 22.200 56 8 7 26.900 16.100 57 1 8 18.900 -3.800 58 2 8 24.900 -3.100 59 3 8 22.200 2.400 60 4 8 13.200 16.200 61 5 8 9.200 24.400 62 6 8 19.400 14.400 63 7 8 35.600 4.500 64 8 8 25.300 17.700 #