2024-03-20 REL RCSB RCSB RCSB 2019-03-05 2019-03-27 2019-06-26 2024-03-20 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM092895 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM107214 United States RNA polymerase II elongation complex arrested at a CPD lesion Lahiri I Leshziner AE RNA polymerase, CPD, elongation complex, streptavidin grids, transcription, transferase-DNA-RNA complex Lahiri I Xu J Han BG Oh J Wang D DiMaio F Leschziner AE 3.1 angstrom structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids. J.Struct.Biol. US 207 270 278 2019 31200019 doi:10.1016/j.jsb.2019.06.004 1095-8657 0803 JSBIEM 6o6c FULLOVERLAP RNA polymerase II elongation complex stalled at a CPD lesion RNA polymerase II elongation complex stalled at a CPD lesion 0 1 2 3 4 5 6 7 8 9 10 11 12 13 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 II subunit RPB2 Saccharomyces cerevisiae 0.138937297 1 LEVO MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTE SDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDS ESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVED GFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDH FGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSE WGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV EDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT NTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN EGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE GRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA KLLFQELMAMNITPRLYTDRSRDF P08518 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Saccharomyces cerevisiae 0.035330457 1 LEVO MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQL EYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAK KGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW P16370 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Saccharomyces cerevisiae 0.025117094 1 LEVO MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM P20434 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Saccharomyces cerevisiae 0.017931833999999997 1 LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL P20435 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Saccharomyces cerevisiae 0.016525363 1 LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR P20436 DNA-directed RNA polymerase II subunit RPB9 Saccharomyces cerevisiae 0.014308161 1 LEVO MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS P27999 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Saccharomyces cerevisiae 0.008290732 1 LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD P22139 DNA-directed RNA polymerase II subunit RPB11 Saccharomyces cerevisiae 0.013633493 1 LEVO MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF P38902 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Saccharomyces cerevisiae 0.007729969 1 LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR P40422 RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3') Saccharomyces cerevisiae 0.002934831 1 AUCGAGAGG DNA (5'-D(P*GP*GP*AP*GP*AP*AP*GP*GP*AP*GP*CP*AP*GP*AP*GP*C)-3') Saccharomyces cerevisiae 0.0050462929999999994 1 (DG)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG)(DC)(DA)(DG)(DA)(DG)(DC) DNA DNA (27-MER) Saccharomyces cerevisiae 0.008376361 1 (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) DNA ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.5 Quantifoil R2/2 GOLD 300
The grids had a monolayer of streptavidin crystals on them.
 ETHANE 100 293.15 FEI VITROBOT MARK IV
The sample was manually wicked from the grid. 1.2 uL sample buffer was then applied to the streptavidin side. The grid was then blotted..
FEI TALOS ARCTICA OTHER BRIGHT FIELD FIELD EMISSION GUN 200 2.7 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 6.0 51.7 1 1Y77 C1 FOURIER SPACE 3.1 FSC 0.143 CUT-OFF 61654 PROJECTION MATCHING RELION 3.0 PROJECTION MATCHING RELION 3.0 emd_0633.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 -0.1602947 0.28207877 -0.0000902388 0.004448481 1.16 1.16 1.16 0.0509 AUTHOR RNA polymerase II elongation complex stalled at a CPD lesion FLEXIBLE FIT REAL