6GMH

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  

  • 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.,Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany. patrick.cramer@mpibpc.mpg.de.,Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen, Germany.,University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RPB1
A
1970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
Find proteins for I3LJR4 (Sus scrofa)
Go to Gene View: POLR2A
Go to UniProtKB:  I3LJR4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
B
1174Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for I3LGP4 (Sus scrofa)
Go to Gene View: POLR2B
Go to UniProtKB:  I3LGP4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit C
C
275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
Find proteins for I3LCH3 (Sus scrofa)
Go to Gene View: POLR2C
Go to UniProtKB:  I3LCH3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit D
D
142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
Find proteins for A0A287ADR4 (Sus scrofa)
Go to Gene View: POLR2D
Go to UniProtKB:  A0A287ADR4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit E
E
210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
Find proteins for I3LSI7 (Sus scrofa)
Go to Gene View: POLR2E
Go to UniProtKB:  I3LSI7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit F
F
127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
Find proteins for F1SKN8 (Sus scrofa)
Go to Gene View: POLR2F
Go to UniProtKB:  F1SKN8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit G
G
172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa)
Go to Gene View: POLR2G
Go to UniProtKB:  I3LJZ9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
Find proteins for I3LCB2 (Sus scrofa)
Go to Gene View: POLR2H
Go to UniProtKB:  I3LCB2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
Find proteins for P60899 (Sus scrofa)
Go to Gene View: POLR2I
Go to UniProtKB:  P60899
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RPB10
J
67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
Find proteins for A0A287B432 (Sus scrofa)
Go to Gene View: POLR2L
Go to UniProtKB:  A0A287B432
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPB11
K
117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
Find proteins for F1RKE4 (Sus scrofa)
Go to Gene View: POLR2J
Go to UniProtKB:  F1RKE4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RPB12
L
58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
Find proteins for I3LN51 (Sus scrofa)
Go to Gene View: POLR2K
Go to UniProtKB:  I3LN51
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT6,Transcription elongation factor SPT6,Transcription elongation factor SPT6
M
1726Homo sapiensMutation(s): 0 
Gene Names: SUPT6H (KIAA0162, SPT6H)
Find proteins for Q7KZ85 (Homo sapiens)
Go to Gene View: SUPT6H
Go to UniProtKB:  Q7KZ85
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
CTR9,RNA polymerase-associated protein CTR9 homolog,RNA polymerase-associated protein CTR9 homolog
Q
1178Homo sapiensMutation(s): 0 
Gene Names: CTR9 (KIAA0155, SH2BP1)
Find proteins for Q6PD62 (Homo sapiens)
Go to Gene View: CTR9
Go to UniProtKB:  Q6PD62
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
LEO1,LEO1,RNA polymerase-associated protein LEO1
U
776N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
PAF1,RNA polymerase II-associated factor 1 homolog,RNA polymerase II-associated factor 1 homolog
V
613N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 61
W
305Homo sapiensMutation(s): 0 
Gene Names: WDR61
Find proteins for Q9GZS3 (Homo sapiens)
Go to Gene View: WDR61
Go to UniProtKB:  Q9GZS3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
CDC73
X
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT4
Y
121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1 (SPT4H, SUPT4H)
Find proteins for P63272 (Homo sapiens)
Go to Gene View: SUPT4H1
Go to UniProtKB:  P63272
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT5
Z
1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H (SPT5, SPT5H)
Find proteins for O00267 (Homo sapiens)
Go to Gene View: SUPT5H
Go to UniProtKB:  O00267
Entity ID: 14
MoleculeChainsLengthOrganism
Non-template DNAN48synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
RNAP46synthetic construct
Entity ID: 17
MoleculeChainsLengthOrganism
Template DNAT48synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
UNK
Query on UNK
M, Q, U, V, X
L-PEPTIDE LINKINGC4 H9 N O2

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TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Experimental preparation