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: https://doi.org/10.1038/s41586-018-0440-4
  • Primary Citation of Related Structures:  
    6GME, 6GMH

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RPB11,970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LJR4 (Sus scrofa)
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UniProt GroupI3LJR4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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UniProt GroupI3LGP4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit C275Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D142Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287ADR4 (Sus scrofa)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LSI7 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit F127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit G172Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCB2 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1067Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RPB11117Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RPB1258Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
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UniProt GroupA0A4X1TRS6
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT6,Transcription elongation factor SPT6,Transcription elongation factor SPT61,726Homo sapiensMutation(s): 0 
Gene Names: SUPT6HKIAA0162SPT6H
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZ85 (Homo sapiens)
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GTEx:  ENSG00000109111 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
CTR9,RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein CTR9 homologP [auth Q]1,178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198730 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
LEO1,LEO1,RNA polymerase-associated protein LEO1R [auth U]776Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166477 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PAF1,RNA polymerase II-associated factor 1 homolog,RNA polymerase II-associated factor 1 homologS [auth V]613Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000006712 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 61T [auth W]305Homo sapiensMutation(s): 0 
Gene Names: WDR61
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GTEx:  ENSG00000140395 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
CDC73U [auth X]16Homo sapiensMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4V [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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GTEx:  ENSG00000213246 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5W [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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Find proteins for O00267 (Homo sapiens)
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GTEx:  ENSG00000196235 
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA48synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNAO [auth P]46synthetic construct
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Entity ID: 17
MoleculeChains LengthOrganismImage
Template DNAQ [auth T]48synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth C]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth B],
BA [auth C],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth L],
GA [auth Y],
X [auth A],
Y [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
Z [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

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  (Full details and data files)

  • 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