2024-05-15 REL PDBe PDBe PDBe 2017-07-18 2017-08-16 2017-09-13 2024-05-15 German Research Foundation SFB860, SPP1935 Germany European Research Council TRANSREGULON Germany Volkswagen Foundation Germany Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC3 Bernecky C Plitzko JM Cramer P RNA polymerase II, transcription elongation, TRANSCRIPTION Bernecky C Plitzko JM Cramer P Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nat. Struct. Mol. Biol. US 24 809 815 2017 28892040 doi:10.1038/nsmb.3465 1545-9985 EMD-3815 other EM volume EMD-3816 other EM volume EMD-3818 other EM volume EMD-3819 other EM volume 5oik FULLOVERLAP RNA polymerase II-DSIF elongation complex RNA polymerase II-DSIF elongation complex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 0.69 RNA polymerase II 1 1 2 3 4 5 6 7 8 9 10 11 12 Bos taurus 0.52 DSIF 1 16 17 Homo sapiens 0.13 DNA-RNA synthetic construct 1 13 14 15 synthetic construct 0.04 DNA-directed RNA polymerase II subunit RPB1 Bos taurus 0.21743606199999999 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 PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDDEN 2.7.7.6 DNA-directed RNA polymerase subunit beta Bos taurus 0.134041422 1 LEVO MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEE PPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTY CLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNF IGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLL AFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAA IADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHI DQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA VDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL EGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV A5PJW8 2.7.7.6 DNA-directed RNA polymerase II subunit RPB3 Bos taurus 0.031466098 1 LEVO MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVD KLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELR LRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN Q3T0Q3 Polymerase (RNA) II (DNA directed) polypeptide D Bos taurus 0.016347254999999998 1 LEVO MAAGGSDPRSGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETI ASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY Q1JQ91 DNA-directed RNA polymerases I, II, and III subunit RPABC1 Bos taurus 0.024514219 1 LEVO MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEP KVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELL ARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ Q2T9T3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 Bos taurus 0.014491025999999999 1 LEVO MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVM VELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD F2Z4C9 DNA-directed RNA polymerase II subunit RPB7 Bos taurus 0.019314282999999998 1 LEVO MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI GSLMDDYLGLVS Q5E9B8 Uncharacterized protein Bos taurus 0.017162273 1 LEVO MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDD RPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF F2Z4H3 DNA-directed RNA polymerase II subunit RPB9 Bos taurus 0.014507204999999999 1 LEVO MEPDGTYEPGIVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPR TEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE Q32P73 DNA-directed RNA polymerases I, II, and III subunit RPABC5 Bos taurus 0.007655122999999999 1 LEVO MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK Q32P78 DNA-directed RNA polymerase II subunit RPB11 Bos taurus 0.013310283999999999 1 LEVO MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE Q32P79 DNA-directed RNA polymerases I, II, and III subunit RPABC4 Bos taurus 0.007018243999999999 1 LEVO MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR Q3ZBC0 DNA (43-MER) synthetic construct 0.013303563 1 (DG)(DG)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DT)(DT)(DC)(DT)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DG) (DA)(DT)(DC) DNA RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3') synthetic construct 0.016081696 1 UAACGAGAUCAUAACAUUUGAACAAGAAUAUAUAUACAUAAAGACCAGGC DNA (43-MER) synthetic construct 0.013178483 1 (DG)(DA)(DT)(DC)(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DA)(DA) (DG)(DC)(DC)(DT)(DG)(DG)(DT)(DC)(DT)(DA)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT) (DG)(DC)(DC) DNA Transcription elongation factor SPT4 Homo sapiens 0.013210200999999998 1 Escherichia coli BL21(DE3) LEVO MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNF KPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT P63272 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 ZINC ION 6.5409e-05 8 ZN MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.25 7.25 5.0 HEPES 150.0 NaCl sodium chloride 0.01 ZnCl2 zinc chloride 1.0 dithiothreitol
pH was adjusted at 25 degrees Celsius
 Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.6 0.6 3.6 3.6 37000.0 37037.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum 0 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1-33 1 2549 9.9 33.0
Movies were aligned and binned to the physical pixel size of 1.35 angstroms.
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