2024-05-15 REL PDBe PDBe PDBe 2018-11-19 2019-01-02 2019-01-02 2024-05-15 European Research Council Transregulon (693023) Germany European Molecular Biology Organization ALTF-725-2014 Germany German Research Foundation SFB1064 Germany German Research Foundation SFB860 Germany Farnung L Vos SM Nucleosome, elongation, chromatin, RNA polymerase II, TRANSCRIPTION Farnung L Vos SM Cramer P Nat Commun UK 9 5432 5432 2018 30575770 doi:10.1038/s41467-018-07870-y 2041-1723 6i84 FULLOVERLAP Complex of S. cerevisiae RNA polymerase II and X. leaves NCP Complex of S. cerevisiae RNA polymerase II and X. leaves NCP 0 1 2 3 4 5 6 7 9 10 11 12 13 14 16 17 18 19 8 15 Complex of S. cerevisiae RNA polymerase II and X. leaves NCP 1 1 2 5 6 Xenopus laevis Complex of S. cerevisiae RNA polymerase II and X. leaves NCP 1 7 8 9 10 11 12 13 14 16 17 18 15 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Complex of S. cerevisiae RNA polymerase II and X. leaves NCP 1 3 4 19 synthetic construct Histone H3.2 Xenopus laevis 0.015435125999999999 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P84233 Histone H2A type 1 Xenopus laevis 0.014109436 2 Escherichia coli LEVO MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK P06897 DNA (170-MER) synthetic construct 0.052041214999999995 1 (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG)(DA)(DT)(DA)(DT)(DA)(DG)(DG)(DA)(DA)(DT)(DA)(DA)(DC)(DA)(DG)(DG)(DA) (DT)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DG) DNA DNA (158-MER) synthetic construct 0.049537551 1 (DT)(DC)(DC)(DT)(DG)(DT)(DT)(DA)(DT)(DT)(DC)(DC)(DT)(DA)(DT)(DA)(DT)(DC)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC) (DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT) DNA Histone H4 Xenopus laevis 0.011394426 2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62799 Histone H2B 1.1 Xenopus laevis 0.013655948 2 Escherichia coli LEVO MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAH YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 DNA-directed RNA polymerase II subunit RPB1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 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 (strain ATCC 204508 / S288c) 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 (strain ATCC 204508 / S288c) 0.038809113 1 LEVO MGSHHHHHHSNSGLNDIFEAQKIEWHEDTGMSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVE VETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIG HPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYE DPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDV MMTGAEQDPYSNASQMGNTGSGGYDNAW P16370 DNA-directed RNA polymerase II subunit RPB4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.025451190999999998 1 LEVO MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKK HLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETV GAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY P20433 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.025117094 1 LEVO MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWV EFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM P20434 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.017931833999999997 1 LEVO MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRA TTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL P20435 DNA-directed RNA polymerase II subunit RPB7 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.019081053 1 LEVO MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI GSIKEDYLGAI P34087 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.016525363 1 LEVO MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWR PPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR P20436 DNA-directed RNA polymerase II subunit RPB9 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.014308161 1 LEVO MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS P27999 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.008290732 1 LEVO MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD P22139 DNA-directed RNA polymerase II subunit RPB11 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.013633493 1 LEVO MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG YDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF P38902 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.007729969 1 LEVO MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR P40422 RNA synthetic construct 0.0031379079999999996 1 UCUCACUGGA ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 7.4 Quantifoil, UltrAuFoil GOLD ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 46.0 1 C1 4.4 FSC 0.143 CUT-OFF 49703 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_4429_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.01601642 0.056836754 0.0000844374 0.0037007297 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Multi-Body refinement, Pol II body (Half-map 2) emd_4429_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.017037012 0.064862646 0.00024986998 0.0028874842 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Multi-Body refinement, NCP body (Half-map 1) emd_4429_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.007965947 0.053010523 0.000011149036 0.0032581121 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Multi-Body refinement, Pol II body emd_4429_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.008094583 0.05031242 0.0002903437 0.0027658234 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Multi-Body refinement, NCP body emd_4429_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.016405905 0.056529343 0.00008029739 0.003715444 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Multi-Body refinement, Pol II body (Half-map 1) emd_4429_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.040229578 0.09701496 0.0000279962 0.004242378 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Postprocessed map of Pol II-NCP refinement emd_4429_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.018677203 0.06523282 0.00025658816 0.0028841714 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Multi-Body refinement, NCP body (Half-map 1) emd_4429_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.011691798 0.056916244 0.00003042068 0.0034281244 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Half map 2 of main map emd_4429_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.0 336.0 336.0 90.0 90.0 90.0 X Y Z -0.013702855 0.052507322 0.00002557172 0.0034381724 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4429:::: Half map 1 of main map