EMDB-16833: Structure of the mammalian Pol II-SPT6-Elongin complex, lacking t...

Basic information

Entry

Database: EMDB / ID: EMD-16833

• Title: Structure of the mammalian Pol II-SPT6-Elongin complex, lacking the ELOA latch (global map for composite map 2)
• Map data: Global map for the Pol II-SPT6-Elongin (NoN) complex. Used in generation of the composite map 2

Sample

• Complex: The Pol II-SPT6-Elongin transcription elongation complex
  • Protein or peptide: x 16 types
  • DNA: x 2 types
  • RNA: x 1 types

• Keywords: Transcription elongation / Elongin / RNA polymerase II / TRANSCRIPTION

Function / homology

Function:

regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / nucleosome organization / regulation of mRNA processing / Cytosolic sensors of pathogen-associated DNA / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / blastocyst formation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / target-directed miRNA degradation / elongin complex / RNA Polymerase III Abortive And Retractive Initiation / VCB complex / : / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Cul5-RING ubiquitin ligase complex / RNA Polymerase I Transcription Termination / transcription elongation-coupled chromatin remodeling / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Viral Messenger RNA Synthesis / Cul2-RING ubiquitin ligase complex / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / tRNA transcription by RNA polymerase III / site of DNA damage / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of translational initiation / RNA polymerase II activity / organelle membrane / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / transcription-coupled nucleotide-excision repair / mRNA transport / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / translation initiation factor binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere

Domain/homology:

RNA polymerase II transcription factor SIII, subunit A / RNA polymerase II transcription factor SIII (Elongin) subunit A / HHH domain 9 / HHH domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / F-box domain profile. / F-box domain / TFIIS/LEDGF domain superfamily / RNA-binding domain, S1 / RuvA domain 2-like / Elongin B / Elongin-C / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit Rpo11 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1

Component:

RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Elongin-A / Elongin-C / Elongin-B / Transcription elongation factor SPT6

• Biological species: Homo sapiens (human) / Sus scrofa (pig) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 2.86 Å
• Authors: Chen Y / Kokic G / Dienemann C / Dybkov O / Urlaub H / Cramer P

Funding support

European Union, Germany, 3 items

Organization	Grant number	Country
European Research Council (ERC)	882357	European Union
German Research Foundation (DFG)	SFB860	Germany
German Research Foundation (DFG)	EXC 2067/1-390729940	Germany

• Citation: Journal: Nat Struct Mol Biol / Year: 2023; Title: Structure of the transcribing RNA polymerase II-Elongin complex.; Authors: Ying Chen / Goran Kokic / Christian Dienemann / Olexandr Dybkov / Henning Urlaub / Patrick Cramer / ; Abstract: Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.

History

Deposition	Mar 13, 2023	-
Header (metadata) release	Oct 18, 2023	-
Map release	Oct 18, 2023	-
Update	Dec 27, 2023	-
Current status	Dec 27, 2023	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_16833.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Global map for the Pol II-SPT6-Elongin (NoN) complex. Used in generation of the composite map 2
• Voxel size: X=Y=Z: 1.05 Å

Density

Contour Level	By AUTHOR: 0.012
Minimum - Maximum	-0.045980535 - 0.1090248
Average (Standard dev.)	-0.000052269632 (±0.0027788428)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 440 440 440 Spacing 440 440 440
Cell	A=B=C: 461.99997 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_16833_msk_1.map

Additional map: local resolution filtered map to show the overall...

• File: emd_16833_additional_1.map
• Annotation: local resolution filtered map to show the overall position of the subunits

Half map: half map 2of the global map

• File: emd_16833_half_map_1.map
• Annotation: half map 2of the global map

Half map: half map1 of the global map

• File: emd_16833_half_map_2.map
• Annotation: half map1 of the global map

Sample components

Entire : The Pol II-SPT6-Elongin transcription elongation complex

• Entire: Name: The Pol II-SPT6-Elongin transcription elongation complex

Components

• Complex: The Pol II-SPT6-Elongin transcription elongation complex
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1Polymerase
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2Polymerase
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3Polymerase
  • Protein or peptide: RNA polymerase II subunit D
  • Protein or peptide: RNA polymerase II subunit E
  • Protein or peptide: RNA polymerase II subunit F
  • Protein or peptide: RNA polymerase II subunit G
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
  • Protein or peptide: RNA polymerase II subunit RPB9
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11-aPolymerase
  • Protein or peptide: RNA polymerase II subunit K
  • DNA: Non-template DNA
  • RNA: RNA
  • DNA: Template DNA
  • Protein or peptide: Transcription elongation factor SPT6
  • Protein or peptide: Elongin A
  • Protein or peptide: Elongin CELOC
  • Protein or peptide: Elongin BELOB

Supramolecule #1: The Pol II-SPT6-Elongin transcription elongation complex

• Supramolecule: Name: The Pol II-SPT6-Elongin transcription elongation complex; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19; Details: The map is generated from a sub-class of a Cryo-EM dataset for the Pol II-SPT6-Elongin complex.
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTG RCQTCAGNMT ECPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV D SNNPKIKD ILAKSKGQPK KRLTHVYDLC KGKNICEGGE EMDNKFGVEQ PEGDEDLTKE KG HGGCGRY QPRIRRSGLE LYAEWKHVNE DSQEKKILLS PERVHEIFKR ISDEECFVLG MEP RYARPE WMIVTVLPVP PLSVRPAVVM QGSARNQDDL THKLADIVKI NNQLRRNEQN GAAA HVIAE DVKLLQFHVA TMVDNELPGL PRAMQKSGRP LKSLKQRLKG KEGRVRGNLM GKRVD FSAR TVITPDPNLS IDQVGVPRSI AANMTFAEIV TPFNIDRLQE LVRRGNSQYP GAKYII RDN GDRIDLRFHP KPSDLHLQTG YKVERHMCDG DIVIFNRQPT LHKMSMMGHR VRILPWS TF RLNLSVTTPY NADFDGDEMN LHLPQSLETR AEIQELAMVP RMIVTPQSNR PVMGIVQD T LTAVRKFTKR DVFLERGEVM NLLMFLSTWD GKVPQPAILK PRPLWTGKQI FSLIIPGHI NCIRTHSTHP DDEDSGPYKH ISPGDTKVVV ENGELIMGIL CKKSLGTSAG SLVHISYLEM GHDITRLFY SNIQTVINNW LLIEGHTIGI GDSIADSKTY QDIQNTIKKA KQDVIEVIEK A HNNELEPT PGNTLRQTFE NQVNRILNDA RDKTGSSAQK SLSEYNNFKS MVVSGAKGSK IN ISQVIAV VGQQNVEGKR IPFGFKHRTL PHFIKDDYGP ESRGFVENSY LAGLTPTEFF FHA MGGREG LIDTAVKTAE TGYIQRRLIK SMESVMVKYD ATVRNSINQV VQLRYGEDGL AGES VEFQN LATLKPSNKA FEKKFRFDYT NERALRRTLQ EDLVKDVLSN AHIQNELERE FERMR EDRE VLRVIFPTGD SKVVLPCNLL RMIWNAQKIF HINPRLPSDL HPIKVVEGVK ELSKKL VIV NGDDPLSRQA QENATLLFNI HLRSTLCSRR MAEEFRLSGE AFDWLLGEIE SKFNQAI AH PGEMVGALAA QSLGEPATQM TLNTFHYAGV SAKNVTLGVP RLKELINISK KPKTPSLT V FLLGQSARDA ERAKDILCRL EHTTLRKVTA NTAIYYDPNP QSTVVAEDQE WVNVYYEMP DFDVARISPW LLRVELDRKH MTDRKLTMEQ IAEKINAGFG DDLNCIFNDD NAEKLVLRIR IMNSDENKM QEEEEVVDKM DDDVFLRCIE SNMLTDMTLQ GIEQISKVYM HLPQTDNKKK I IITEDGEF KALQEWILET DGVSLMRVLS EKDVDPVRTT SNDIVEIFTV LGIEAVRKAL ER ELYHVIS FDGSYVNYRH LALLCDTMTC RGHLMAITRH GVNRQDTGPL MKCSFEETVD VLM EAAAHG ESDPMKGVSE NIMLGQLAPA GTGCFDLLLD AEKCKYGMEI PTNIPGLGAA GPTG MFFGS APSPMGGISP AMTPWNQGAT PAYGAWSPSV GSGMTPGAAG FSPSAASDAS GFSPG YSPA WSPTPGSPGS PGPSSPYIPS PGGAMSPSYS PTSPAYEPRS PGGYTPQSPS YSPTSP SYS PTSPSYSPTS PNYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSP TS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPS Y SPTSPNYSPT SPNYTPTSPS YSPTSPSYSP TSPNYTPTSP NYSPTSPSYS PTSPSYSPT SPSYSPSSPR YTPQSPTYTP SSPSYSPSSP SYSPTSPKYT PTSPSYSPSS PEYTPTSPKY SPTSPKYSP TSPKYSPTSP TYSPTTPKYS PTSPTYSPTS PVYTPTSPKY SPTSPTYSPT S PKYSPTSP TYSPTSPKGS TYSPTSPGYS PTSPTYSLTS PAISPDDSDE EN

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MCSTNLSQAL AYFRAGANLT AASLWAGFRG SRRIFWERRK RKSLCLALRP GGACWRWLLA VSCVSLRGL GAPGSCANMY DADEDMQYDE DDDEITPDLW QEACWIVISS YFDEKGLVRQ Q LDSFDEFI QMSVQRIVED APPIDLQAEA QHASGEVEEP PRYLLKFEQI YLSKPTHWER DG APSPMMP NEARLRNLTY SAPLYVDITK TVIKEGEEQL QTQHQKTFIG KIPIMLRSTY CLL NGLTDR DLCELNECPL DPGGYFIING SEKVLIAQEK MATNTVYVFA KKDSKYAYTG ECRS CLENS SRPTSTIWVS MLARGGQGAK KSAIGQRIVA TLPYIKQEVP IIIVFRALGF VSDRD ILEH IIYDFEDPEM MEMVKPSLDE AFVIQEQNVA LNFIGSRGAK PGVTKEKRIK YAKEVL QKE MLPHVGVSDF CETKKAYFLG YMVHRLLLAA LGRRELDDRD HYGNKRLDLA GPLLAFL FR GMFKNLLKEV RIYAQKFIDR GKDFNLELAI KTRIISDGLK YSLATGNWGD QKKAHQAR A GVSQVLNRLT FASTLSHLRR LNSPIGRDGK LAKPRQLHNT LWGMVCPAET PEGHAVGLV KNLALMAYIS VGSQPSPILE FLEEWSMENL EEISPAAIAD ATKIFVNGCW VGIHKDPEQL MNTLRKLRR QMDIIVSEVS MIRDIREREI RIYTDAGRIC RPLLIVEKQK LLLKKRHIDQ L KEREYNNY SWQDLVASGV VEYIDTLEEE TVMLAMTPDD LQEKEVAYCS TYTHCEIHPS MI LGVCASI IPFPDHNQSP RNTYQSAMGK QAMGVYITNF HVRMDTLAHV LYYPQKPLVT TRS MEYLRF RELPAGINSI VAIASYTGYN QEDSVIMNRS AVDRGFFRSV FYRSYKEQES KKGF DQEEV FEKPTRETCQ GMRHAIYDKL DDDGLIAPGV RVSGDDVIIG KTVTLPENED ELEGT NRRY TKRDCSTFLR TSETGIVDQV MVTLNQEGYK FCKIRVRSVR IPQIGDKFAS RHGQKG TCG IQYRQEDMPF TCEGITPDII INPHAIPSRM TIGHLIECLQ GKVSANKGEI GDATPFN DA VNVQKISNLL SDYGYHLRGN EVLYNGFTGR KITSQIFIGP TYYQRLKHMV DDKIHSRA R GPIQILNRQP MEGRSRDGGL RFGEMERDCQ IAHGAAQFLR ERLFEASDPY QVHVCNLCG IMAIANTRTH TYECRGCRNK TQISLVRMPY ACKLLFQELM SMSIAPRMMS V

UniProtKB: DNA-directed RNA polymerase subunit beta

Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLG LIPLTSDDIV DKLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD L ISNSPRVI PVTSRNRDND PSDYVEQDDI LIVKLRKGQE LRLRAYAKKG FGKEHAKWNP TA GVAFEYD PDNALRHTVY PKPEEWPKSE YSELDEDESQ APYDPNGKPE RFYYNVESCG SLR PETIVL SALSGLKKKL SDLQTQLSHE IQSDVLTIN

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

Macromolecule #4: RNA polymerase II subunit D

• Macromolecule: Name: RNA polymerase II subunit D / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MWGPAQPYSD SALSPKPRPF RAVFRGSALP FPAVRVEVRG RSMAAGGSDP RAGDVEEDAS QLIFPKEFE TAETLLNSEV HMLLEHRKQQ NESAEDEQEL SEVFMKTLNY TARFSRFKNR E TIASVRSL LLQKKLHKFE LACLANLCPE TAEESKALIP SLEGRFEDEE LQQILDDIQT KR SFQY

UniProtKB: RNA polymerase II subunit D

Macromolecule #5: RNA polymerase II subunit E

• Macromolecule: Name: RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPT DQMFVFFPEE PKVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV D MAPKYILE QFLQQELLIN ITEHELVPEH VVMTKEEVTE LLARYKLREN QLPRIQAGDP VA RYFGIKR GQVVKIIRPS ETAGRYITYR LVQ

UniProtKB: DNA-directed RNA polymerase II subunit E

Macromolecule #6: RNA polymerase II subunit F

• Macromolecule: Name: RNA polymerase II subunit F / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTR ALQIAMCAPV MVELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG V DELIISD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

Macromolecule #7: RNA polymerase II subunit G

• Macromolecule: Name: RNA polymerase II subunit G / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYP VKYKAIVFRP FKGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF D PNSNPPCY KTMDEDIVIQ QDDEIRLKIV GTRVDKNDIF AIGSLMDDYL GLVS

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC3; type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGT LDDGEYNPTD DRPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG G LLMRLQGD ANNLHGFEVD SRVYLLMKKL AF

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

Macromolecule #9: RNA polymerase II subunit RPB9

• Macromolecule: Name: RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQII ADVSQDPTLP RTEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC G HRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC5; type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEH KIIIRVQTTP DYSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

UniProtKB: DNA-directed RNA polymerase II subunit RPB11-a

Macromolecule #12: RNA polymerase II subunit K

• Macromolecule: Name: RNA polymerase II subunit K / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)

Sequence

String:

MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: RNA polymerase II, I and III subunit K

Macromolecule #16: Transcription elongation factor SPT6

• Macromolecule: Name: Transcription elongation factor SPT6 / type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MSDFVESEAE ESEEEYNDEG EVVPRVTKKF VEEEDDDEEE EEENLDDQDE QGNLKGFIND DDDEDEGEE DEGSDSGDSE DDVGHKKRKR TSFDDRLEDD DFDLIEENLG VKVKRGQKYR R VKKMSDDE DDDEEEYGKE EHEKEAIAEE IFQDGEGEEG QEAMEAPMAP PEEEEEDDEE SD IDDFIVD DDGQPLKKPK WRKKLPGYTD AALQEAQEIF GVDFDYDEFE KYNEYDEELE EEY EYEDDE AEGEIRVRPK KTTKKRVSRR SIFEMYEPSE LESSHLTDQD NEIRATDLPE RFQL RSIPV KGAEDDELEE EADWIYRNAF ATPTISLQES CDYLDRGQPA SSFSRKGPST IQKIK EALG FMRNQHFEVP FIAFYRKEYV EPELHINDLW RVWQWDEKWT QLRIRKENLT RLFEKM QAY QYEQISADPD KPLADGIRAL DTTDMERLKD VQSMDELKDV YNHFLLYYGR DIPKMQN AA KASRKKLKRV REEGDEEGEG DEAEDEEQRG PELKQASRRD MYTICQSAGL DGLAKKFG L TPEQFGENLR DSYQRHETEQ FPAEPLELAK DYVCSQFPTP EAVLEGARYM VALQIAREP LVRQVLRQTF QERAKLNITP TKKGRKDVDE AHYAYSFKYL KNKPVKELRD DQFLKICLAE DEGLLTTDI SIDLKGVEGY GNDQTYFEEI KQFYYRDEFS HQVQEWNRQR TMAIERALQQ F LYVQMAKE LKNKLLAEAK EYVIKACSRK LYNWLRVAPY RPDQQVEEDD DFMDENQGKG IR VLGIAFS SARDHPVFCA LVNGEGEVTD FLRLPHFTKR RTAWREEERE KKAQDIETLK KFL LNKKPH VVTVAGENRD AQMLIEDVKR IVHELDQGQQ LSSIGVELVD NELAILYMNS KKSE AEFRD YPPVLRQAVS LARRIQDPLI EFAQVCSSDE DILCLKFHPL QEHVVKEELL NALYC EFIN RVNEVGVDVN RAIAHPYSQA LIQYVCGLGP RKGTHLLKIL KQNNTRLESR TQLVTM CHM GPKVFMNCAG FLKIDTASLG DSTDSYIEVL DGSRVHPETY EWARKMAVDA LEYDESA ED ANPAGALEEI LENPERLKDL DLDAFAEELE RQGYGDKHIT LYDIRAELSC RYKDLRTA Y RSPNTEEIFN MLTKETPETF YIGKLIICNV TGIAHRRPQG ESYDQAIRND ETGLWQCPF CQQDNFPELS EVWNHFDSGS CPGQAIGVKT RLDNGVTGFI PTKFLSDKVV KRPEERVKVG MTVHCRIMK IDIEKFSADL TCRTSDLMDR NNEWKLPKDT YYDFDAEAAD HKQEEDMKRK Q QRTTYIKR VIAHPSFHNI NFKQAEKMME TMDQGDVIIR PSSKGENHLT VTWKVSDGIY QH VDVREEG KENAFSLGAT LWINSEEFED LDEIVARYVQ PMASFARDLL NHKYYQDCSG GDR KKLEEL LIKTKKEKPT FIPYFICACK ELPGKFLLGY QPRGKPRIEY VTVTPEGFRY RGQI FPTVN GLFRWFKDHY QDPVPGITPS SSSRTRTPAS INATPANINL ADLTRAVNAL PQNMT SQMF SAIAAVTGQG QNPNATPAQW ASSQYGYGGS GGGSSAYHVF PTPAQQPVAT PLMTPS YSY TTPSQPITTP QYHQLQASTT PQSAQAQPQP SSSSRQRQQQ PKSNSHAAID WGKMAEQ WL QEKEAERRKQ KQRLTPRPSP SPMIESTPMS IAGDATPLLD EMDR

UniProtKB: Transcription elongation factor SPT6

Macromolecule #17: Elongin A

• Macromolecule: Name: Elongin A / type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MHGGRSCGPR TRREPSSGEE AAPVTAMAAE SALQVVEKLQ ARLAANPDPK KLLKYLKKLS TLPITVDIL AETGVGKTVN SLRKHEHVGS FARDLVAQWK KLVPVERNAE PDEQDFEKSN S RKRPRDAL QKEEEMEGDY QETWKATGSR SYSPDHRQKK HRKLSELERP HKVSHGHERR DE RKRCHRM SPTYSSDPES SDYGHVQSPP SCTSPHQMYV DHYRSLEEDQ EPIVSHQKPG KGH SNAFQD RLGASQERHL GEPHGKGVVS QNKEHKSSHK DKRPVDAKSD EKASVVSREK SHKA LSKEE NRRPPSGDNA REKPPSSGVK KEKDREGSSL KKKCLPPSEA ASDNHLKKPK HRDPE KAKL DKSKQGLDSF DTGKGAGDLL PKVKEKGSNN LKTPEGKVKT NLDRKSLGSL PKVEET DME DEFEQPTMSF ESYLSYDQPR KKKKKIVKTS ATALGDKGLK KNDSKSTGKN LDSVQKL PK VNKTKSEKPA GADLAKLRKV PDVLPVLPDL PLPAIQANYR PLPSLELISS FQPKRKAF S SPQEEEEAGF TGRRMNSKMQ VYSGSKCAYL PKMMTLHQQC IRVLKNNIDS IFEVGGVPY SVLEPVLERC TPDQLYRIEE YNHVLIEETD QLWKVHCHRD FKEERPEEYE SWREMYLRLQ DAREQRLRV LTKNIQFAHA NKPKGRQAKM AFVNSVAKPP RDVRRRQEKF GTGGAAVPEK I KIKPAPYP MGSSHASASS ISFNPSPEEP AYDGPSTSSA HLAPVVSSTV SYDPRKPTVK KI APMMAKT IKAFKNRFSR R

UniProtKB: Elongin-A

Macromolecule #18: Elongin C

• Macromolecule: Name: Elongin C / type: protein_or_peptide / ID: 18 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHV LSKVCMYFTY KVRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

Macromolecule #19: Elongin B

• Macromolecule: Name: Elongin B / type: protein_or_peptide / ID: 19 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARP QAPATVGLAF RADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

Macromolecule #13: Non-template DNA

• Macromolecule: Name: Non-template DNA / type: dna / ID: 13 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)

Sequence

String:

ccattgaGAG CGGcccttgt gttcaGGAGC CAGCAGGGAG CTGGGAGC

Macromolecule #15: Template DNA

• Macromolecule: Name: Template DNA / type: dna / ID: 15 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)

Sequence

String:

GCTCCCAGCT CCCTGCTGGC TCCGAGTGGG TTCTGCCGCT CTCAATGG

Macromolecule #14: RNA

• Macromolecule: Name: RNA / type: rna / ID: 14
• Source (natural): Organism: synthetic construct (others)

Sequence

String:

uuaaGGaauU AAGUCGUGCG UCUAAUAACC GGAGAGGGAA CCCACU

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Grid: Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.1
• Vitrification: Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.5 µm / Nominal defocus min: 0.35000000000000003 µm
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.09 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: NONE
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118642

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: OTHER