Structure of active transcription elongation complex Pol II-DSIF (SPT5-KOW5) alone, Map 11, Global map

2025-07-09 REL PDBe 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 DATABASE_REFERENCES citation _citation.pdbx_database_id_PubMed _citation.title DATABASE_REFERENCES citation database_2 _citation.journal_volume _citation.page_first _citation.page_last _database_2.pdbx_DOI _database_2.pdbx_database_accession DATA_COLLECTION chem_comp_atom chem_comp_bond em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification PDBe PDBe 2021-05-18 2021-07-14 2021-07-14 2025-07-09 German Research Foundation (DFG) SFB860 Germany German Research Foundation (DFG) EXC 2067/1-390729940 Germany European Research Council (ERC) Advanced Grant CHROMATRANS 693023 Germany German Research Foundation (DFG) SFB1286 Germany Structure of active transcription elongation complex Pol II-DSIF (SPT5-KOW5) alone, Map 11, Global map Chen Y Vos SM Dienemann C Ninov M Urlaub H Cramer P Pol II, Super elongation complex, ELL2, EAF1, TRANSCRIPTION Chen Y Vos SM Dienemann C Ninov M Urlaub H Cramer P Allosteric transcription stimulation by RNA polymerase II super elongation complex. Mol.Cell US 81 3386 3399.e10 2021 34265249 doi:10.1016/j.molcel.2021.06.019 1097-2765 2168 MOCEFL EMD-12966 other EM volume EMD-12967 other EM volume EMD-12968 other EM volume EMD-12969 other EM volume EMD-12970 other EM volume EMD-12971 other EM volume EMD-12972 other EM volume EMD-12973 other EM volume 7ol0 FULLOVERLAP Transcription elongation complex of RNA polymerase II with elongation factors DSIF (SPT5-KOW5) Transcription elongation complex of RNA polymerase II with elongation factors DSIF (SPT5-KOW5) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

This is a for map for Pol II-DSIF alone class. In this map, ELL2, EAF1, SPT4 are not visible. For SPT5, only the KOW5 domain is visible.

Sus scrofa DNA-directed RNA polymerase II subunit RPB1 Sus scrofa 0.217450078 1 LEVO MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTE CPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEM DNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDN ELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNID RLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV MNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGIL CKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPF GFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR NSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLL FNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLG VPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMD DDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSN DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPW NQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAY EPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSP SYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYT PTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN DNA-directed RNA polymerase subunit beta Sus scrofa 0.142426125 1 LEVO MCSTNLSQALAYFRAGANLTAASLWAGFRGSRRIFWERRKRKSLCLALRPGGACWRWLLAVSCVSLRGLGAPGSCANMYD ADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEEPPR YLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLL NGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSMLARG GQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGS RGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFL FRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLR RLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIAD ATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQL KEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNT YQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDR GFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGT NRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITP DIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFI GPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCG IMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV I3LGP4 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Sus scrofa 0.031439074 1 LEVO MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVD KLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELR LRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN I3LCH3 RNA polymerase II subunit D Sus scrofa 0.020962620999999997 1 LEVO MWGPAQPYSDSALSPKPRPFRAVFRGSALPFPAVRVEVRGRSMAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVH MLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSL EGRFEDEELQQILDDIQTKRSFQY A0A287ADR4 DNA-directed RNA polymerase II subunit E Sus scrofa 0.024644318 1 LEVO MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEP KVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELL ARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ I3LSI7 DNA-directed RNA polymerase II subunit F Sus scrofa 0.014477001 1 LEVO MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVM VELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD F1SKN8 DNA-directed RNA polymerase II subunit RPB7 Sus scrofa 0.019314282999999998 1 LEVO MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI GSLMDDYLGLVS I3LJZ9 DNA-directed RNA polymerases I, II, and III subunit RPABC3 Sus scrofa 0.017162273 1 LEVO MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDD RPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF A0A4X1ULF2 DNA-directed RNA polymerase II subunit RPB9 Sus scrofa 0.014541220999999998 1 LEVO MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPR TEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE P60899 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Sus scrofa 0.007655122999999999 1 LEVO MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK A0A4X1VYD0 RNA_pol_L_2 domain-containing protein Sus scrofa 0.013310283999999999 1 LEVO MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE A0A4X1UK25 RNA polymerase II subunit K Sus scrofa 0.007018243999999999 1 LEVO MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR I3LN51 Transcription elongation factor SPT5 Homo sapiens 0.12114547699999999 1 Escherichia coli BL21(DE3) LEVO MSDSEDSNFSEEEDSERSSDGEEAEVDEERRSAAGSEKEEEPEDEEEEEEEEEYDEEEEEEDDDRPPKKPRHGGFILDEA DVDDEYEDEDQWEDGAEDILEKEEIEASNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSVGETVYGGSDE LSDDITQQQLLPGVKDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIE GVGNLRLGYWNQQMVPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDYDRIKARM SLKDWFAKRKKFKRPPQRLFDAEKIRSLGGDVASDGDFLIFEGNRYSRKGFLFKSFAMSAVITEGVKPTLSELEKFEDQP EGIDLEVVTESTGKEREHNFQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRKYFKMGDHVKV IAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSETASGVDVGGQHEWGELVQLDPQTVGVIVRLERETFQV LNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCKT RHLVLAGGSKPRDVTNFTVGGFAPMSPRISSPMHPSAGGQRGGFGSPGGGSGGMSRGRGRRDNELIGQTVRISQGPYKGY IGVVKDATESTARVELHSTCQTISVDRQRLTTVGSRRPGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTP HYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPG TPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSP GGYNPHTPGSGIEQNSSDWVTTDIQVKVRDTYLDTQVVGQTGVIRSVTGGMCSVYLKDSEKVVSISSEHLEPITPTKNNK VKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKLLEA O00267 RNA HIV whole-genome vector AA1305#18 0.015076016999999999

The last nucleotide 47 (A) in the sample was extended to the 3' of the original scaffolding RNA (46-mer) during sample preparation in the presence of ATP.

1 ACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCACUA Non-template DNA HIV whole-genome vector AA1305#18 0.014672441 1 (DG)(DT)(DA)(DC)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DG)(DA) (DG)(DT)(DG)(DA)(DC)(DC)(DT)(DT)(DA)(DA)(DG)(DC)(DC)(DT)(DC)(DA)(DA)(DT)(DA)(DA) (DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC) DNA Template DNA HIV whole-genome vector AA1305#18 0.01493458 1 (DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DT)(DA)(DT)(DT)(DG)(DA)(DG)(DG)(DC)(DT)(DT) (DA)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DG)(DG)(DT)(DT)(DC)(DA)(DA)(DG)(DG)(DT)(DA)(DC) (DT)(DA)(DG)(DT)(DG)(DT)(DA)(DC) DNA MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 8 ZN singleParticle particle 7.4 ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 BIOQUANTUM (6k x 4k) COUNTING 43.21 1 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio model created by CryoSPARC

3.0 FSC 0.143 CUT-OFF 194785 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_12974.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 315.0 315.0 315.0 90.0 90.0 90.0 X Y Z -0.08875522 0.15978946 0.00019237849 0.005338669 1.05 1.05 1.05 0.018 AUTHOR ::::EMDATABANK.org::::EMD-12974:::: Map 11, main map for Pol II-DSIF (SPT5-KOW5) alone model REAL emd_12974_msk_1.map emd_12974_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 315.0 315.0 315.0 90.0 90.0 90.0 X Y Z -0.028396338 0.07435648 0.00019398081 0.003442494 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-12974:::: half map 2 for map 11 emd_12974_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 315.0 315.0 315.0 90.0 90.0 90.0 X Y Z -0.029108467 0.072936155 0.00019077616 0.0034448036 1.05 1.05 1.05 AUTHOR ::::EMDATABANK.org::::EMD-12974:::: half map 1 for map 11