Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex

2025-12-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update DATA_COLLECTION em_admin _em_admin.last_update PDBe PDBe 2019-04-23 2019-11-13 2019-12-18 2025-12-17 German Research Foundation SFB860 Germany German Research Foundation SPP1935 Germany German Federal Ministry for Education and Research EXC 2067/1- 390729940 Germany European Research Council TRANSREGULON Germany Volkswagen Foundation Germany German Research Foundation Fi 573 7-2 Germany German Research Foundation Fi 573 18-1 Germany Structure of Vaccinia Virus DNA-dependent RNA polymerase elongation complex Hillen HS Bartuli J Vaccinia, RNA polymerase, Transcription, Gene expression, VIRAL PROTEIN Hillen HS Bartuli J Grimm C Dienemann C Bedenk K Szalay AA Fischer U Cramer P Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes. Cell 179 1525 2019 31835031 doi:10.1016/j.cell.2019.11.023 1097-4172 EMD-4888 other EM volume EMD-4868 other EM volume EMD-4890 other EM volume EMD-4891 other EM volume 6rid FULLOVERLAP EMDB EMD-4889 associated EM volume

EMDB EMD-4888 other EM volume EMDB EMD-4868 other EM volume EMDB EMD-4890 other EM volume EMDB EMD-4891 other EM volume PDB 6RFG unspecified PDB 6RFL unspecified PDB 6RIE unspecified Vaccinia Virus DNA-dependent RNA polymerase elongation complex Vaccinia Virus DNA-dependent RNA polymerase elongation complex 0 1 2 3 4 5 6 7 8 9 10 11 0.45 DNA-directed RNA polymerase subunits 1 1 3 4 5 6 7 8 Vaccinia virus GLV-1h68 DNA-dependent RNA polymerase subunit rpo132 1 2 Vaccinia virus GLV-1h68 Nucleic acids 1 9 10 11 Vaccinia virus GLV-1h68 DNA-dependent RNA polymerase subunit rpo147 Vaccinia virus GLV-1h68 0.146995703 1 Vaccinia virus LEVO MAVISKVTYSLYDQKEINATDIIISHVKNDDDIGTVKDGRLGAMDGALCKTCGKTELECFGHWGKVSIYKTHIVKPEFIS EIIRLLNHICIHCGLLRSREPYSDDINLKELSGHALRRLKDKILSKKKSCWNSECMQPYQKITFSKKKVCFVNKLDDINV PNSLIYQKLISIHEKFWPLLEIHQYPANLFYTDYFPIPPLIIRPAISFWIDSIPKETNELTYLLGMIVKNCNLNADEQVI QKAVIEYDDIKIISNNTTSINLSYITSGKNNMIRSYIVARRKDQTARSVIGPSTSITVNEVGMPAYIRNTLTEKIFVNAF TVDKVKQLLASNQVKFYFNKRLNQLTRIRQGKFIKNKIHLLPGDWVEVAVQEYTSIIFGRQPSLHRYNVIASSIRATEGD TIKISPGIANSQNADFDGDEEWMILEQNPKAVIEQSILMYPTTLLKHDIHGAPVYGSIQDEIVAAYSLFRIQDLCLDEVL NILGKYGREFDPKGKCKFSGKDIYTYLIGEKINYPGLLKDGEIIANDVDSNFVVAMRHLSLAGLLSDHKSNVEGINFIIK SSYVFKRYLSIYGFGVTFKDLRPNSTFTNKLEAINVEKIELIKEAYAKYLNDVRDGKIVPLSKALEADYVESMLSNLTNL NIREIEEHMRQTLIDDPDNNLLKMAKAGYKVNPTELMYILGTYGQQRIDGEPAETRVLGRVLPYYLPDSKDPEGRGYILN SLTKGLTGSQYYFSMLVARSQSTDIVCETSRTGTLARKIIKKMEDMVVDGYGQVVIGNTLIKYAANYTKILGSVCKPVDL IYPDESMTWYLEISALWNKIKQGFVYSQKQKLAKKTLAPFNFLVFVKPTTEDNAIKVKDLYDMIHNVIDDVREKYFFTVS NIDFMEYIFLTHLNPSRIRITKETAITIFEKFYEKLNYTLGGGTPIGIISAQVLSEKFTQQALSSFHTTEKSGAVKQKLG FNEFNNLTNLSKNKTEIITLVSDDISKLQSVKINFEFVCLGELNPNITLRKETDKYVVDIIVNRLYIKRAEITELVVEYM IERFISFSVIVKEWGMETFIEDEDNIRFTVYLNFVEPEELNLSKFMMVLPGAANKGKISKFKIPISDYTGYDDFNQTKKL NKMTVELMNLKELGSFDLENVNVYPGVWNTYDIFGIEAAREYLCEAMLNTYGEGFDYLYQPCDLLASLLCASYEPESVNK FKFGAASTLKRATFGDNKALLNAALHKKSEPINDNSSCHFFSKVPNIGTGYYKYFIDLGLLMRMERKLSDKISSQKIKEM EETEDF B9U1I2 2.7.7.6 DNA-dependent RNA polymerase subunit rpo132 Vaccinia virus GLV-1h68 0.133526859 1 Vaccinia virus LEVO MKKNTNSEMDQRLGYKFLVPDPKAGVFYRPLHFQYVSYSNFILHRLHEILTVKRPLLSFKNNTERIMIEISNVKVTPPDY SPIIASIKGKSYDALATFTVNIFKEVMTKEGISITKISSYEGKDSHLIKIPLLIGYGNKNPLDTAKYLVPNVIGGVFINK QSVEKVGINLVEKITTWPKFRVVKPNSFTFSFSSVSPPNVLPTRYRHYKISLDISQLEALNISSTKTFITVNIVLLSQYL SRVSLEFIRRSLSYDMPPEVVYLVNAIIDSAKRITESITDFNIDTYINDLVEAEHIKQKSQLTINEFKYEMLHNFLPHMN YTPDQLKGFYMISLLRKFLYCIFHTSRYPDRDSMVCHRILTYGKYFETLAHDELENYIGNIRNDIMNNHKNRGTYAVNIH VLTTPGLNHAFSSLLSGKFKKSDGSYRTHPHYSWMQNISIPRSVGFYPDQVKISKMFSVRKYHPSQYLYFCSSDVPERGP QVGLVSQLSVLSSITNILTSEYLDLEKKICEYIRSYYKDDISYFETGFPITIENALVASLNPNMICDFVTDFRRRKRMGF FGNLEVGITLVRDHMNEIRINIGAGRLVRPFLVVDNGELMMDVCPELESRLDDMTFSDIQKEFPHVIEMVDIEQFTFSNV CESVQKFRMMSKDERKQYDLCDFPAEFRDGYVASSLVGINHNSGPRAILGCAQAKQAISCLSSDIRNKIDNGIHLMYPER PIVISKALETSKIAANCFGQHVTIALMSYKGINQEDGIIIKKQFIQRGGLDIVTAKKHQVEIPLENFNNKERDRSNAYSK LESNGLVRLNAFLESGDAMARNISSRTLEDDFARDNQISFDVSEKYTDMYKSRVERVQVELTDKVKVRVLTMKERRPILG DKFTTRTSQKGTVAYVADETELPYDENGITPDVIINSTSIFSRKTISMLIEVILTAAYSAKPYNNKGENRPVCFPSSNET SIDTYMQFAKQCYEHSNPKLSDEELSDKIFCEKILYDPETDKPYASKVFFGPIYYLRLRHLTQDKATVRCRGKKTKLIRQ ANEGRKRGGGIKFGEMERDCLIAHGAANTITEVLKDSEEDYQDVYVCENCGDIAAQIKGINTCLRCSKLNLSPLLTKIDT THVSKVFLTQMNARGVKVKLDFERRPPSFYKPLDKVDLKPSFLV B9U1Q1 2.7.7.6 DNA-directed RNA polymerase 35 kDa subunit Vaccinia virus GLV-1h68 0.035430676 1 Vaccinia virus LEVO MQHPREENSIVVELEPSLATFIKQGFNNLVKWPLLNIGIVLSNTSTAVNEEWLTAVEHIPTMKIFYKHIHKILTREMGFL VYLKRSQSERDNYITLYDFDYYIIDKDTNSVTMVDKPTELKETLLHVFQEYRLKSSQTIELIAFSSGTVINEDIVSKLTF LDVEVFNREYNNVKTIIDPDFVFRSPFIVISPMGKLTFFVEVYSWFDFKSCFKDIIDFLEGALIANIHNHMIKVGNCDET VSSYNPESGMLFVNDLMTMNIVNFFGCNSRLESYHRFDMTKVDVELFIKALSDACKKILSASNRL B9U1R2 2.7.7.6 DNA-directed RNA polymerase subunit Vaccinia virus GLV-1h68 0.02136574 1 Vaccinia virus LEVO MNQYNVKYLAKILCLKTEIARDPYAVINRNVLLRYTTDIEYNDLVTLITVRHKIDSMKTVFQVFNESSINYTPVDDDYGE PIIITSYLQKGHNKFPVNFLYIDVVISDLFPSFVRLDTTETNIVNSVLQTGDGKKTLRLPKMLETEIVVKILYRPNIPLK IVRFFRNNMVTGVEIADRSVISVAD B9U1I0 2.7.7.6 DNA-directed RNA polymerase 19 kDa subunit Vaccinia virus GLV-1h68 0.019020087999999997 1 Vaccinia virus LEVO MADTDDIIDYESDDLTEYEDDEEEEEDGESLETSDIDPKSSYKIVESASTHIEDAHSNLKHIGNHISALKRRYTRRISLF EIAGIIAESYNLLQRGRLPLVSEFSDETMKQNMLHVIIQEIEEGSCPIVIEKNGELLSVNDFDKDGLKFHLDYIIKIWKL QKRY B9U1M4 2.7.7.6 DNA-dependent RNA polymerase subunit rpo18 Vaccinia virus GLV-1h68 0.017917195 1 Vaccinia virus LEVO MSSFVTNGYLSVTLEPHELTLDIKTNIRNAVYKTYLHREISGKMAKKIEIREDVELPLGEIVNNSVVINVPCVITYAYYH VGDIVRGTLNIEDESNVTIQCGDLICKLSRDSGTVSFSDSKYCFFRNGNAYDNGSEVTAVLMEAQQGIESSFVFLANIVD S B9U1K4 2.7.7.6 DNA-dependent RNA polymerase subunit rpo7 Vaccinia virus GLV-1h68 0.007299715 1 Vaccinia virus LEVO MVFQLVCSTCGKDISHERYKLIIRKKSLKDVLVSVKNECCRLKLSTQIEPQRNLTVQPLLDIN B9U1G3 2.7.7.6 DNA-directed RNA polymerase 30 kDa polypeptide Vaccinia virus GLV-1h68 0.029834358999999998 1 Vaccinia virus LEVO MENVYISSYSSNEQTSMAVAATDIRELLSQYVDDANLEDLIEWAMEKSSKYYIKNIGNTKSNIEETKFESKNNIGIEYSK DSRNKLSYRNKPSIATNLEYKTLCDMIKGTSGTEKEFLRYLLFGIKCIKKGVEYNIDKIKDVSYNDYFNVLDEKYNTPCP NCKSRNTTPMMIQTRAADEPPLVRHACRDCKQHFKPPKFRAFRNLNVTTQSIHENKEITEILPDNNPSPPESPEPASPID DGLIRATFDRNDEPPEDDE B9U1D1 2.7.7.6 Non-template strand DNA Vaccinia virus 0.014775472999999999 1 (DG)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DG)(DG)(DC)(DA)(DT)(DC)(DC)(DC)(DA)(DT)(DG)(DC) (DG)(DT)(DT)(DG)(DA)(DG)(DG)(DA)(DC)(DT)(DC)(DT)(DT)(DA)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DA)(DT)(DA)(DA)(DG)(DT)(DC) DNA Template strand DNA Vaccinia virus 0.014786516999999999 1 (DG)(DA)(DC)(DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DA)(DA)(DG)(DA)(DG) (DT)(DC)(DC)(DA)(DG)(DC)(DC)(DA)(DA)(DT)(DG)(DA)(DC)(DA)(DG)(DA)(DT)(DG)(DC)(DC) (DT)(DC)(DA)(DT)(DA)(DG)(DC)(DC) DNA RNA Vaccinia virus 0.009742849 1 GAGUUGUAAUAACAAGGGAAAUGUCAUUGG MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 4 ZN singleParticle particle 7.5 ETHANE 95 277 FEI VITROBOT MARK II FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 2.7 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 QUANTUM (4k x 4k) COUNTING 1 4958 1.02 1 632458 RELION 3.0 Warp PHASE FLIPPING AND AMPLITUDE CORRECTION Ab initio model generated by cryoSPARC. 1 C1 FOURIER SPACE 2.9 FSC 0.143 CUT-OFF RELION 3.0 110733 ANGULAR RECONSTITUTION RELION 3.0 ANGULAR RECONSTITUTION RELION 3.0 4 RELION 3.0 emd_4889.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 356.99997 356.99997 356.99997 90.0 90.0 90.0 X Y Z -0.102170415 0.17589764 0.00017017401 0.0036384354 1.05 1.05 1.05 0.028 AUTHOR ::::EMDATABANK.org::::EMD-4889:::: AB INITIO MODEL REAL emd_4889_msk_1.map emd_4889_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 356.99997 356.99997 356.99997 90.0 90.0 90.0 X Y Z -0.027468303 0.07459932 -0.000014175208 0.0022007828 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4889:::: emd_4889_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 356.99997 356.99997 356.99997 90.0 90.0 90.0 X Y Z -0.04570399 0.0863697 -0.0000035356868 0.0040778182 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4889:::: emd_4889_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 356.99997 356.99997 356.99997 90.0 90.0 90.0 X Y Z -0.038228355 0.09046876 -0.000005490782 0.004074713 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-4889::::