6GMH

Structure of activated transcription complex Pol II-DSIF-PAF-SPT6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of activated transcription complex Pol II-DSIF-PAF-SPT6.

Vos, S.M.Farnung, L.Boehning, M.Wigge, C.Linden, A.Urlaub, H.Cramer, P.

(2018) Nature 560: 607-612

  • DOI: 10.1038/s41586-018-0440-4
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elong ...

    Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RPB1A1970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
Find proteins for I3LJR4 (Sus scrofa)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaB1174Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit CC275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
Find proteins for I3LCH3 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit DD142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
Find proteins for A0A287ADR4 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit EE210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
Find proteins for I3LSI7 (Sus scrofa)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit FF127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
Find proteins for F1SKN8 (Sus scrofa)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit GG172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
Find proteins for I3LCB2 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9I125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
Find proteins for P60899 (Sus scrofa)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RPB10J67Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RPB12L58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT6,Transcription elongation factor SPT6,Transcription elongation factor SPT6M1726Homo sapiensMutation(s): 0 
Gene Names: SUPT6HKIAA0162SPT6H
Find proteins for Q7KZ85 (Homo sapiens)
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PHAROS  Q7KZ85
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
CTR9,RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein CTR9 homologQ1178Homo sapiensMutation(s): 0 
Gene Names: CTR9
Find proteins for Q6PD62 (Homo sapiens)
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PHAROS  Q6PD62
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
LEO1,LEO1,RNA polymerase-associated protein LEO1U776Homo sapiensMutation(s): 0 
Gene Names: LEO1
Find proteins for Q8WVC0 (Homo sapiens)
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PHAROS  Q8WVC0
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
PAF1,RNA polymerase II-associated factor 1 homolog,RNA polymerase II-associated factor 1 homologV613Homo sapiensMutation(s): 0 
Gene Names: PAF1
Find proteins for Q8N7H5 (Homo sapiens)
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PHAROS  Q8N7H5
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 61W305Homo sapiensMutation(s): 0 
Gene Names: WDR61
Find proteins for Q9GZS3 (Homo sapiens)
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PHAROS  Q9GZS3
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
CDC73X16Homo sapiensMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT4Y121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
Find proteins for P63272 (Homo sapiens)
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PHAROS  P63272
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT5Z1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
Find proteins for O00267 (Homo sapiens)
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PHAROS  O00267
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPB11K117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
Find proteins for F1RKE4 (Sus scrofa)
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  • Reference Sequence

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Entity ID: 14
MoleculeChainsLengthOrganism
Non-template DNAN48synthetic construct

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Entity ID: 15
MoleculeChainsLengthOrganism
RNAP46synthetic construct

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Entity ID: 17
MoleculeChainsLengthOrganism
Template DNAT48synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, I, J, L, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany693023
European Molecular Biology OrganizationGermanyALTF-725-2014
Volkswagen FoundationGermany--
German Research FoundationGermanyDFG SFB860

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-12-18
    Changes: Other