Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state)

2025-05-28 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2023-08-18 2024-01-24 2024-01-24 2025-05-28 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM092895 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM145296 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM102362 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM092895 United States Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Sarsam RD Lahiri I Leschziner AE RNA Polymerase II, Rad26, CPD lesion, Transcription-coupled DNA repair, TRANSCRIPTION, TRANSCRIPTION-DNA-RNA complex Sarsam RD Xu J Lahiri I Gong W Li Q Oh J Zhou Z Hou P Chong J Hao N Li S Wang D Leschziner AE Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair. Proc.Natl.Acad.Sci.USA US 121 e2314245121 e2314245121 2024 38194460 doi:10.1073/pnas.2314245121 1091-6490 0040 PNASA6 8tvy FULLOVERLAP Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Saccharomyces cerevisiae DNA-directed RNA polymerase II subunit RPB1 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 P04050 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 polymerase II subunit RPB4 Saccharomyces cerevisiae 0.025451190999999998 1 LEVO MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK HLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETV GAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY A0A6A5PTI6 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 P20435 DNA-directed RNA polymerase II subunit RPB7 Saccharomyces cerevisiae 0.019081053 1 LEVO MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI GSIKEDYLGAI A0A6A5Q270 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 RAD26 isoform 1 Saccharomyces cerevisiae 0.12471057 1 Escherichia coli LEVO MEDKEQQDNAKLENNESLKDLGVNVLSQSSLEEKIANDVTNFSNLQSLQQEETRLERSKTALQRYVNKKNHLTRKLNNTT RISVKQNLRDQIKNLQSDDIERVLKDIDDIQSRIKELKEQVDQGAENKGSKEGLQRPGETEKEFLIRTGKITAFGHKAGF SLDTANREYAKNDEQKDEDFEMATEQMVENLTDEDDNLSDQDYQMSGKESEDDEEEENDDKILKELEDLRFRGQPGEAKD DGDELYYQERLKKWVKQRSCGSQRSSDLPEWRRPHPNIPDAKLNSQFKIPGEIYSLLFNYQKTCVQWLYELYQQNCGGII GDEMGLGKTIQVIAFIAALHHSGLLTGPVLIVCPATVMKQWCNEFQHWWPPLRTVILHSMGSGMASDQKFKMDENDLENL IMNSKPSDFSYEDWKNSTRTKKALESSYHLDKLIDKVVTDGHILITTYVGLRIHSDKLLKVKWQYAVLDEGHKIRNPDSE ISLTCKKLKTHNRIILSGTPIQNNLTELWSLFDFIFPGKLGTLPVFQQQFVIPINIGGYANATNIQVQTGYKCAVALRDL ISPYLLRRVKADVAKDLPQKKEMVLFCKLTKYQRSKYLEFLHSSDLNQIQNGKRNVLFGIDILRKICNHPDLLDRDTKRH NPDYGDPKRSGKMQVVKQLLLLWHKQGYKALLFTQSRQMLDILEEFISTKDPDLSHLNYLRMDGTTNIKGRQSLVDRFNN ESFDVFLLTTRVGGLGVNLTGANRIIIFDPDWNPSTDMQARERAWRIGQKREVSIYRLMVGGSIEEKIYHRQIFKQFLTN RILTDPKQKRFFKIHELHDLFSLGGENGYSTEELNEEVQKHTENLKNSKSEESDDFEQLVNLSGVSKLESFYNGKEKKEN SKTEDDRLIEGLLGGESNLETVMSHDSVVNSHAGSSSSNIITKEASRVAIEAVNALRKSRKKITKQYEIGTPTWTGRFGK AGKIRKRDPLKNKLTGSAAILGNITKSQKEASKEARQENYDDGITFARSKEINSNTKTLENIRAYLQKQNNFFSSSVSIL NSIGVSLSDKEDVIKVRALLKTIAQFDKERKGWVLDEEFRNNNAS A0A8H4BZR7 DNA (NTS) synthetic construct 0.014494314 1 (DC)(DT)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC)(DT)(DC)(DA)(DT)(DA)(DT)(DT)(DT)(DC)(DA) (DT)(DT)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG) (DC)(DA)(DG)(DA)(DG)(DC)(DG) DNA DNA (TS) synthetic construct 0.014275127 1 (DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC)(DT)(DC)(DC)(DT)(DT)(DC)(DT)(DC)(DC)(TTD)(DT) (DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DG)(DA)(DT) (DC)(DA)(DA)(DC)(DT)(DA)(DG) DNA RNA synthetic construct 0.003264036 1 AUCGAGAGGA Transcription elongation factor 1 homolog Saccharomyces cerevisiae 0.009635077999999998 1 Escherichia coli LEVO MGKRKKSTRKPTKRLVQKLDTKFNCLFCNHEKSVSCTLDKKNSIGTLSCKICGQSFQTRINSLSQPVDVYSDWFDAVEEV NSGRG A0A6A5PV14 ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.4 ETHANE FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.6 2.5 GATAN K2 SUMMIT (4k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1Y77 3.1 FSC 0.143 CUT-OFF 50000 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION emd_41655.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 445.44 445.44 445.44 90.0 90.0 90.0 X Y Z -4.178593 6.2754583 0.004196712 0.10511014 1.16 1.16 1.16 0.417 AUTHOR ::::EMDATABANK.org::::EMD-41655:::: Filtered map emd_41655_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 445.44 445.44 445.44 90.0 90.0 90.0 X Y Z -0.06266967 0.15900552 0.00010026551 0.0039109066 1.16 1.16 1.16 AUTHOR ::::EMDATABANK.org::::EMD-41655:::: Focused refinement on Rad26 emd_41655_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 445.44 445.44 445.44 90.0 90.0 90.0 X Y Z -0.90211993 2.507154 -0.00024756455 0.0829841 1.16 1.16 1.16 AUTHOR ::::EMDATABANK.org::::EMD-41655:::: emd_41655_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 445.44 445.44 445.44 90.0 90.0 90.0 X Y Z -2.0328047 2.9479473 0.000009530293 0.23333593 1.16 1.16 1.16 AUTHOR ::::EMDATABANK.org::::EMD-41655:::: emd_41655_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 445.44 445.44 445.44 90.0 90.0 90.0 X Y Z -1.9301939 3.067482 -0.00003028584 0.23189312 1.16 1.16 1.16 AUTHOR ::::EMDATABANK.org::::EMD-41655::::