{"data_9RYB":{"entry":{"id":["9RYB"]},"audit_conform":{"dict_name":["mmcif_pdbx.dic"],"dict_version":["5.414"],"dict_location":["http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic"]},"database_2":{"database_id":["PDB","WWPDB","EMDB"],"database_code":["9RYB","D_1292149366","EMD-54374"],"pdbx_database_accession":["pdb_00009ryb",null,null],"pdbx_DOI":["10.2210/pdb9ryb/pdb",null,null]},"pdbx_audit_revision_history":{"ordinal":[1,2,3,4,5,6,7],"data_content_type":["Structure model","EM metadata","FSC","Half map","Half map","Image","Primary map"],"major_revision":[1,1,1,1,1,1,1],"minor_revision":[0,0,0,0,0,0,0],"revision_date":["2026-05-27","2026-05-27","2026-05-27","2026-05-27","2026-05-27","2026-05-27","2026-05-27"],"part_number":[null,null,null,1,2,null,null]},"pdbx_audit_revision_details":{"ordinal":[1,2,3,4,5,6,7],"revision_ordinal":[1,2,3,4,5,6,7],"data_content_type":["Structure model","EM metadata","FSC","Half map","Half map","Image","Primary 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volume"]},"pdbx_contact_author":{"id":[3,4],"email":["dongwang@ucsd.edu","peijun.zhang@strubi.ox.ac.uk"],"name_first":["D.","P."],"name_last":["Wang","Zhang"],"name_mi":[null,null],"role":["principal investigator/group leader","principal investigator/group leader"],"identifier_ORCID":["0000-0002-2829-1546","0000-0003-1803-691X"]},"audit_author":{"name":["Li, Q.","Yi, G.","Zhang, P.","Wang, D."],"pdbx_ordinal":[1,2,3,4],"identifier_ORCID":["0000-0002-8583-3620","0009-0004-6509-4893","0000-0003-1803-691X","0000-0002-2829-1546"]},"citation":{"abstract":[null],"abstract_id_CAS":[null],"book_id_ISBN":[null],"book_publisher":[null],"book_publisher_city":[null],"book_title":[null],"coordinate_linkage":[null],"country":["US"],"database_id_Medline":[null],"details":[null],"id":["primary"],"journal_abbrev":["Mol.Cell"],"journal_id_ASTM":["MOCEFL"],"journal_id_CSD":["2168"],"journal_id_ISSN":["1097-2765"],"journal_full":[null],"journal_issue":[null],"journal_volume":[null],"language":[null],"page_first":[null],"page_last":[null],"title":["Sub-2 angstrom cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis."],"year":[2026],"database_id_CSD":[null],"pdbx_database_id_DOI":["10.1016/j.molcel.2026.04.007"],"pdbx_database_id_PubMed":[42066756],"pdbx_database_id_patent":[null],"unpublished_flag":[null]},"citation_author":{"citation_id":["primary","primary","primary","primary","primary","primary","primary","primary"],"name":["Li, Q.","Yi, G.","Wu, Y.","Xu, S.","Chong, J.","Huang, X.","Zhang, P.","Wang, D."],"ordinal":[1,2,3,4,5,6,7,8],"identifier_ORCID":[null,null,null,null,null,null,null,null]},"entity":{"id":["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20"],"type":["polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","polymer","non-polymer","non-polymer","non-polymer","non-polymer","water"],"src_method":["man","man","man","man","man","man","man","man","man","man","man","man","man","man","man","syn","syn","syn","syn","nat"],"pdbx_description":["DNA-directed RNA polymerase II subunit RPB1","DNA-directed RNA polymerase II subunit RPB2","DNA-directed RNA polymerase II subunit RPB3","DNA-directed RNA polymerase II subunit RPB4","DNA-directed RNA polymerases I, II, and III subunit RPABC1","DNA-directed RNA polymerases I, II, and III subunit RPABC2","DNA-directed RNA polymerase II subunit RPB7","DNA-directed RNA polymerases I, II, and III subunit RPABC3","DNA-directed RNA polymerase II subunit RPB9","DNA-directed RNA polymerases I, II, and III subunit RPABC5","DNA-directed RNA polymerase II subunit RPB11","DNA-directed RNA polymerases I, II, and III subunit RPABC4","DNA (74-mer)","RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*GP*GP*GP*AP*GP*AP*AP*G)-3')","DNA (74-MER)","MAGNESIUM ION","ZINC ION","POTASSIUM ION","DIPHOSPHATE","water"],"formula_weight":[191821.578,138937.297,35330.457,25451.191,25117.094,17931.834,19081.053,16525.363,14308.161,8290.732,13633.493,7729.969,22851.645,6283.85,22582.428,24.305,65.409,39.098,173.943,18.015],"pdbx_number_of_molecules":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,8,1,1,712],"pdbx_ec":["2.7.7.6","2.7.7.6",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"pdbx_mutation":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"pdbx_fragment":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"details":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]},"entity_name_com":{"entity_id":["1","2","3","4","5","6","7","8","9","10","11","12"],"name":["RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220","RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide","RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide","RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide","RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide","RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide","RNA polymerase II subunit B7,B16","RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide","RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9","RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide","RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide","RNA polymerases I,II,and III subunit ABC4,ABC10-alpha"]},"entity_poly":{"entity_id":["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15"],"type":["polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polypeptide(L)","polydeoxyribonucleotide","polyribonucleotide","polydeoxyribonucleotide"],"nstd_linkage":["no","no","no","no","no","no","no","no","no","no","no","no","no","no","no"],"nstd_monomer":["no","no","no","no","no","no","no","no","no","no","no","no","no","no","no"],"pdbx_seq_one_letter_code":["MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGH\nFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQ\nLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP\nVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGR\nPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHP\nGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA\nDFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVI\nPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQ\nVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR\nFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFV\nENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEK\nQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI\nRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQ\nAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYL\nEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA\nAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIE\nRVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDG\nSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA\nFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEAT\nSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP\nTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP\nSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR","MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTE\nSDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDS\nESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI\nRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVED\nGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDH\nFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS\nQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSE\nWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV\nEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND\nLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ\nKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT\nNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG\nLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN\nEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE\nGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA\nKLLFQELMAMNITPRLYTDRSRDF","MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQL\nEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAK\nKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV\nDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW","MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK\nHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETV\nGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY","MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV\nEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE\nKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM","MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA\nTTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL","MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK\nPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI\nGSIKEDYLGAI","MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR\nPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR","MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS\nREN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