2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Polymer geometry

the DNA/RNA hybrid was refined with an updated library for nucleotide stereochemistry. this library, which was not available at the time of the initial deposition, yielded an improved geometry

STRUCTURE_SUMMARY atom_site citation database_PDB_caveat em_imaging em_software entity entity_name_com entity_src_nat ndb_struct_conf_na ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_contact_author pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_validate_close_contact pdbx_validate_peptide_omega pdbx_validate_polymer_linkage pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond pdbx_validate_torsion struct_conf struct_conn struct_conn_type struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _citation.journal_volume _citation.page_first _citation.page_last _em_imaging.nominal_defocus_max _em_imaging.nominal_defocus_min _em_software.category _em_software.fitting_id _em_software.imaging_id _entity.pdbx_description _entity_src_nat.common_name _pdbx_validate_polymer_linkage.dist _struct_mon_prot_cis.pdbx_omega_angle _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.pdbx_db_accession STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature pdbx_validate_close_contact struct_conn struct_conn_type _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_entry_details.has_protein_modification _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.dist _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.dist _struct_conn_type.id EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update RCSB RCSB 2021-04-27 2022-02-02 2022-02-02 2026-08-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM123233 United States National Institutes of Health/National Cancer Institute (NIH/NCI) CA196539 United States National Institutes of Health/National Institute on Aging (NIH/NIA) AG031862 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U24GM129547 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) S10OD023592 United States Yang C Fujiwara R PIC, TFIIH, transcription, ITC, RNA polymerase II Yang C Fujiwara R Kim HJ Basnet P Zhu Y Gorbea Colon JJ Steimle S Garcia BA Kaplan CD Murakami K Mol.Cell US 82 660 676.e9 2022 35051353 doi:10.1016/j.molcel.2021.12.020 1097-2765 2168 MOCEFL EMD-23904 other EM volume EMD-23905 other EM volume EMD-23906 other EM volume EMD-23907 other EM volume 7ml4 FULLOVERLAP EMDB EMD-23908 associated EM volume EMDB EMD-23904 other EM volume EMDB EMD-23905 other EM volume EMDB EMD-23906 other EM volume EMDB EMD-23907 other EM volume RNA polymerase II initially transcribing complex (ITC) RNA polymerase II initially transcribing complex (ITC) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

composite map assembled from 3 independently refined domains

Saccharomyces cerevisiae Pol II + TFIIB + RNA 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Saccharomyces cerevisiae DNA+TBP+TFIIA+TFIIE+TFIIF 1 1 24 25 26 27 28 29 30 31 Saccharomyces cerevisiae TFIIH 1 16 17 18 19 20 21 22 23 Saccharomyces cerevisiae Transcription initiation factor IIF subunit alpha Saccharomyces cerevisiae 0.08232057000000001 1 LEVO MSRRNPPGSRNGGGPTNASPFIKRDRMRRNFLRMRMGQNGSNSSSPGVPNGDNSRGSLVKKDDPEYAEEREKMLLQIGVE ADAGRSNVKVKDEDPNEYNEFPLRAIPKEDLENMRTHLLKFQSKKKINPVTDFHLPVRLHRKDTRNLQFQLTRAEIVQRQ KEISEYKKKAEQERSTPNSGGMNKSGTVSLNNTVKDGSQTPTVDSVTKDNTANGVNSSIPTVTGSSVPPASPTTVSAVES NGLSNGSTSAANGLDGNASTANLANGRPLVTKLEDAGPAEDPTKVGMVKYDGKEVTNEPEFEEGTMDPLADVAPDGGGRA KRGNLRRKTRQLKVLDENAKKLRFEEFYPWVMEDFDGYNTWVGSYEAGNSDSYVLLSVEDDGSFTMIPADKVYKFTARNK YATLTIDEAEKRMDKKSGEVPRWLMKHLDNIGTTTTRYDRTRRKLKAVADQQAMDEDDRDDNSEVELDYDEEFADDEEAP IIDGNEQENKESEQRIKKEMLQANAMGLRDEEAPSENEEDELFGEKKIDEDGERIKKALQKTELAALYSSDENEINPYLS ESDIENKENESPVKKEEDSDTLSKSKRSSPKKQQKKATNAHVHKEPTLRVKSIKNCVIILKGDKKILKSFPEGEWNPQTT KAVDSSNNASNTVPSPIKQEEGLNSTVAEREETPAPTITEKDIIEAIGDGKVNIKEFGKFIRRKYPGAENKKLMFAIVKK LCRKVGNDHMELKKE P41895 Transcription initiation factor IIF subunit beta Saccharomyces cerevisiae 0.046512355 1 LEVO MSSGSAGAPALSNNSTNSVAKEKSGNISGDEYLSQEEEVFDGNDIENNETKVYEESLDLDLERSNRQVWLVRLPMFLAEK WRDRNNLHGQELGKIRINKSKITLLLNENDNDSIPHEYDLELTKKVVENEYVFTEQNLKKYQQRKKELEADPEKQRQAYL KKQEREEELKKKQQQQKRRNNRKKFNHRVMTDRDGRDRYIPYVKTIPKKTAIVGTVCHECQVMPSMNDPNYHKIVEQRRN IVKLNNKERITTLDETVGVTMSHTGMSMRSDNSNFLKVGREKAKSNIKSIRMPKKEILDYLFKLFDEYDYWSLKGLKERT RQPEAHLKECLDKVATLVKKGPYAFKYTLRPEYKKLKEEERKATLGELADEQTGSAGDNAQGDAEADLEDEIEMEDVV A0A6A5PZ00 DNA-directed RNA polymerase II subunit RPB4 Saccharomyces cerevisiae 0.025451190999999998 1 LEVO MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK HLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETV GAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY A0A6A5PTI6 DNA-directed RNA polymerase II subunit RPB7 Saccharomyces cerevisiae 0.019081053 1 LEVO MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI GSIKEDYLGAI A0A6A5Q270 Transcription initiation factor IIB Saccharomyces cerevisiae 0.038257339999999994 1 LEVO MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVG EASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDE KTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIP RFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKILYEHR DKLVDPQLIANGVVSLDNLPGVEKK P29055 DNA-directed RNA polymerase subunit Saccharomyces cerevisiae 0.191821578 1 LEVO MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGH FGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQ LVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGR PVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHP GAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVI PTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQ VCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFV ENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEK QSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQ AFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYL EPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIE RVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDG SYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEAT SPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR A0A6A5Q1P2 2.7.7.6 DNA-directed RNA polymerase subunit beta Saccharomyces cerevisiae 0.138937297 1 LEVO MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTE SDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDS ESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVED GFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDH FGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSE WGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV EDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT NTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN EGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE GRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA KLLFQELMAMNITPRLYTDRSRDF A0A6A5Q4H2 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Saccharomyces cerevisiae 0.035330457 1 LEVO MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQL EYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAK KGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW A0A6A5Q0Z3 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Saccharomyces cerevisiae 0.025117094 1 LEVO MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM A0A6A5Q456 DNA-directed RNA polymerases I,II,and III subunit RPABC2 Saccharomyces cerevisiae 0.017931833999999997 1 LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL A0A6L0ZRI7 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Saccharomyces cerevisiae 0.016525363 1 LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR A0A6A5Q8C2 DNA-directed RNA polymerase II subunit RPB9 Saccharomyces cerevisiae 0.014308161 1 LEVO MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS A0A7I9EWC2 DNA-directed RNA polymerases II subunit RPABC5 Saccharomyces cerevisiae 0.008290732 1 LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD A0A6A5Q7Q6 DNA-directed RNA polymerase II subunit RPB11 Saccharomyces cerevisiae 0.013633493 1 LEVO MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF A0A6A5Q7A1 DNA-directed RNA polymerases II subunit RPABC4 Saccharomyces cerevisiae 0.007729969 1 LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR A0A6A5PY05 BJ4_G0050160.mRNA.1.CDS.1 Saccharomyces cerevisiae 0.038188438 1 LEVO MLMDEYEENKDMCPICKTDRYLSPDVKFLVNPECYHRICESCVDRIFSLGPAQCPYKGCDKILRKNKFKTQIFDDVEVEK EVDIRKRVFNVFNKTIDDFNGDLVEYNKYLEEVEDIIYKLDHGIDVAKTEEKLRTYEELNKQLIMNNLERSRTEIESFEQ RQKFEKEMKLKKRLLERQIEEEERMNKEWTKKEIVNRLSTTTQDINETIEGVKNTVKLKKSSARRKLEELNRVLKNNPYF NSNVNVQNSRLKDAVPFTPFNGDREAHPRFTLKGSVYNDPFIKDLEHRKEFIASGFNTNYAYERVLTEAFMGLGCVISEE L A0A7I9BTI9 General transcription and DNA repair factor IIH helicase subunit XPD Saccharomyces cerevisiae 0.089899047 1 LEVO MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTVSLLSLTIAYQMHYPEHRKIIYCSRTMSEIE KALVELENLMDYRTKELGYQEDFRGLGLTSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEDPEANVELCEYHE NLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMISLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNI DNVCIESLSLDLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILTDQEEPFVETPVLPQDLLTEA IPGNIRRAEHFVSFLKRLIEYLKTRMKVLHVISETPKSFLQHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALK DIATFATLISTYEEGFLLIIEPYEIENAAVPNPIMRFTCLDASIAIKPVFERFSSVIITSGTISPLDMYPRMLNFKTVLQ KSYAMTLAKKSFLPMIITKGSDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVFFPSYLYMESIVSMWQTMGIL DEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLSVARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLE FMRENYRIRENDFLSFDAMRHAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQGLSDADLNLSTDMAISNTKQF LRTMAQPTDPKDQEGVSVWSYEDLIKHQNSRKDQGGFIENENKEGEQDEDEDEDIEMQ A0A6A5Q1C1 3.6.4.12 General transcription and DNA repair factor IIH subunit TFB4 Saccharomyces cerevisiae 0.037430347999999995 1 LEVO MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKGSIIKVLEALIVFLNAHLAFNSANKVAVIAAYS QGIKYLYPESTSALKASESENKTRSDLKIINS(UNK)(UNK)YRRFRNVDETLVEEIYKLFELEKKQIEQNSQRSTLAGA MSAGLTYVNRISKESVTTSLKSRLLVLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDATN GVYLHVESTEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSVCLCVLSIIPPGNKCPACDSQF DEHVIAKLKRKPVVPRLKAKKKVTKP A0A7I9C5C2 General transcription and DNA repair factor IIH Saccharomyces cerevisiae 0.05202466399999999 1 LEVO MAPVVISESEEDEDRVAITRRTKRQVHFDGEGDDRVDQQQQQHSSSHRDRDKHVQRKKKKRLSNRNLQGSNGGYAWEDEI KRSWDLVKVDDEGDMASLVASIVEARKKRTAKKNITPYQRGIIRSLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEF FDQNPISQMGIIIMRNGLAQLVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVPAHCTREVLIVFGSLS TTDPGDIHQTIDSLVSEKIRVKVLGLSAQVAICKELCKATNYGDESFYKILLDETHLKELFNEAVTPLPVNKINKGFTLV KMGFPTRIFEDTPTFCSCHSKLVYGGYFCPNCHSKVCSLPTVCPCCDLMLILSTHLARSYHHLMPLKTFAEVPTTEKFRS EDCFSCQSRFP(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)SRYR CEDCKQEFCVDCDVFIHEILHNCPGCESKPVIT A0A7I9FQL5 Tfb1 Saccharomyces cerevisiae 0.058722551 1 LEVO MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEV VPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDADIYEEKRRREESAQHTETPMSSSSVTAGTPTPHLDTPQLNNGAPLI NTAKLDDSLSKEKLLTNLKLQQSLLKGNKVLMKVFQETVINAGLPPSEFWSTRIPLLR(UNK)FAL(UNK)(UNK)SQK (UNK)GP(UNK)(UNK)V(UNK)(UNK)(UNK)(UNK)(UNK)P(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)NLSREKILNIFENYPIVKKAYTDNVPKNFKEPEFWARFFSSKLFRKL(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)L (UNK)(UNK)(UNK)(UNK)(UNK)F(UNK)(UNK)K(UNK)(UNK)(UNK)(UNK)LLHPVKKII(UNK)LDGNI (UNK)DDPVVRG(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)VDILKGMNRLSEKMIM(UNK)LK(UNK) (UNK)(UNK)K(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)RVIT(UNK)IKINAKQA(UNK)H(UNK)(UNK)(UNK)EV KSTLPIDLLESCRMLHTTCCEFLKHFAIH(UNK)(UNK)(UNK)(UNK)(UNK)QKQASTVKKLYNHLKDCIEKLNELFQ DVLNGDGESMSNTCTAYLKPVLNSITLATHKYDEYFNEYNNNSN General transcription and DNA repair factor IIH helicase subunit XPB Saccharomyces cerevisiae ATCC 204508 / S288c 0.095461664 1 LEVO MTDVEGYQPKSKGKIFPDMGESFFSSDEDSPATDAEIDENYDDNRETSEGRGERDTGAMVTGLKKPRKKTKSSRHTAADS SMNQMDAKDKALLQDTNSDIPADFVPDSVSGMFRSHDFSYLRLRPDHASRPLWISPSDGRIILESFSPLAEQAQDFLVTI AEPISRPSHIHEYKITAYSLYAAVSVGLETDDIISVLDRLSKVPVAESIINFIKGATISYGKVKLVIKHNRYFVETTQAD ILQMLLNDSVIGPLRIDSDHQVQPPEDVLQQQLQQTAGKPATNVNPNDVEAVFSAVIGGDNEREEEDDDIDAVHSFEIAN ESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAA CTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKVMDFLTGR EWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEANWMELSQKGHIANVQCAEVWCP MTAEFYQEYLRETARKRMLLYIMNPTKFQACQFLIQYHERRGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNIL QNFQYNDQINTIFLSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDTQEMYYST KRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGIEVGDDADNSVGRGSNGHKRFKSKAVRG EGSLSGLAGGEDMAYMEYSTNKNKELKEHHPLIRKMYYKNLKK Q00578 3.6.4.12 General transcription and DNA repair factor IIH subunit TFB5 Saccharomyces cerevisiae 0.00824349 1 LEVO MARARKGALVQCDPSIKALILQIDAKMSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPMDEEENQ Q3E7C1 RNA polymerase II transcription factor B subunit 2 Saccharomyces cerevisiae 0.058602312 1 LEVO MSDYSLKHSVTQYLEEIPQQVQNRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLLDLDKWVNSNGKLQFQNAIKS MKSLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEVQNSFGVVVEENVVSLDLLDEYSANKWETILHFMVGTPLAKIPS EKVLNLLKHSKLMEEVNSTGEFKITNEGFQFLLQEINSQLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKID ALSETQRIMLQDMRDYGLVFQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNREEPSVNEDGANGKSTTDITT SDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQITRESIRRALTNGITADQIIAYL ETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGV LLWKDDKKKKFFISKEGNSQVLDFAKRKLKKKQ A0A6A5Q2X3 Transcription initiation factor IIE subunit beta Saccharomyces cerevisiae 0.037050434 1 LEVO MSKNRDPLLANLNAFKSKVKSAPVIAPAKVGQKKTNDTVITIDGNTRKRTASERAQENTLNSAKNPVLVDIKKEAGSNSS NAISLDDDDDDEDFGSSPSKKVRPGSIAAAALQANQTDISKSHDSSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDKVI ELLKKLDRIEFDPKKGTFKYLSTYDVHSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKT PRYVWYNSGGNLKCIDEEFVKMWENVQLPQFAELPRKLQDLGLKPASVDPATIKRQTKRVEVKKKRQRKGKITNTHMTGI LKDYSHRV A0A6A5PS93 Transcription initiation factor IIA large subunit Saccharomyces cerevisiae 0.032230805 1 LEVO MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFSWDNQFNEGNINGVQNDLNFNLATPG VNSSEFNIKEENTGNEGLILPNINSNNNIPHSGETNINTNTVEATNNSGATLNTNTSGNTNADVTSQPKIEVKPEIELTI NNANITTVENIDDESEKKDDEEKEEDVEKTRKEKEQIEQVKLQAKKEKRSALLDTDEVGSELDDSDDDYLISEGEEDGPD ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV A0A6A5Q2T8 Transcription initiation factor IIA subunit 2 Saccharomyces cerevisiae 0.013473069999999998 1 LEVO MAVPGYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIV KNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE A0A6A5PRZ0 non-template strand DNA Saccharomyces cerevisiae 0.011825692999999998 1 (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DT)(DA) (DT)(DA)(DA)(DA)(DA)(DG)(DC)(DT)(DA)(DT)(DG)(DG)(DA)(DA)(DC)(DG)(DT)(DT) DNA template strand DNA Saccharomyces cerevisiae 0.034207805 1 (DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(DA)(DA)(DC)(DG)(DT)(DT)(DC)(DC)(DA)(DT)(DA)(DG)(DC) (DT)(DT)(DT)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT) DNA TATA-box-binding protein Saccharomyces cerevisiae 0.027042275 1 LEVO MADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSATSGIVPTLQNIVATVTLGCRL DLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNI VGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM P13393 Transcription initiation factor IIE subunit alpha Saccharomyces cerevisiae 0.054804808999999996 1 LEVO MDRPIDDIVKNLLKFVVRGFYGGSFVLVLDAILFHSVLAEDDLKQLLSINKTELGPLIARLRSDRLISIHKQREYPPNSK SVERVYYYVKYPHAIDAIKWKVHQVVQRLKDDLDKNSEPNGYMCPICLTKYTQLEAVQLLNFDRTEFLCSLCDEPLVEDD SGKKNKEKQDKLNRLMDQIQPIIDSLKKIDDSRIEENTFEIALARLIPPQNQSHAAYTYNPKKGSTMFRPGDSAPLPNLM GTALGNDSSRRAGANSQATLHINITTASDEVAQRELQERQAEEKRKQNAVPEWHKQSTIGKTALGRLDNEEEFDPVVTAS AMDSINPDNEPAQETSYQNNRTLTEQEMEERENEKTLNDYYAALAKKQAKLNKEEEEEEEEEEDEEEEEEEEMEDVMDDN DETARENALEDEFEDVTDTAGTAKTESNTSNDVKQESINDKTEDAVNATATASGPSANAKPNDGDDDDDDDDDEMDIEFE DV A0A6A5PTU5 RNA Saccharomyces cerevisiae 0.001649072 1 GAGGA ZINC ION 6.5409e-05 15 ZN MAGNESIUM ION 2.4305e-05 1 MG IRON/SULFUR CLUSTER 0.00035163999999999996 1 SF4 singleParticle particle 7.6 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 45.0 1 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.1 FSC 0.143 CUT-OFF

final map is a composite of 3 individually refined domains

254448 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD RELION 3.1 5OQJ PDB experimental model REAL