6GML

Structure of paused transcription complex Pol II-DSIF-NELF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structure of paused transcription complex Pol II-DSIF-NELF.

Vos, S.M.Farnung, L.Urlaub, H.Cramer, P.

(2018) Nature 560: 601-606

  • DOI: 10.1038/s41586-018-0442-2

  • PubMed Abstract: 
  • Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here ...

    Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we report the cryo-electron microscopy structure of a paused transcription elongation complex containing Sus scrofa Pol II and Homo sapiens DSIF and NELF at 3.2 Å resolution. The structure reveals a tilted DNA-RNA hybrid that impairs binding of the nucleoside triphosphate substrate. NELF binds the polymerase funnel, bridges two mobile polymerase modules, and contacts the trigger loop, thereby restraining Pol II mobility that is required for pause release. NELF prevents binding of the anti-pausing transcription elongation factor IIS (TFIIS). Additionally, NELF possesses two flexible 'tentacles' that can contact DSIF and exiting RNA. These results define the paused state of Pol II and provide the molecular basis for understanding the function of NELF during promoter-proximal gene regulation.


    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
DNA-directed RNA polymerase subunit
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
271Sus 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 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: 5
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: 6
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: 7
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: 8
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
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: 9
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
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: 10
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
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: 14
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor A
U
528Homo sapiensMutation(s): 0 
Gene Names: NELFA (WHSC2)
Find proteins for Q9H3P2 (Homo sapiens)
Go to Gene View: NELFA
Go to UniProtKB:  Q9H3P2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor B,Negative elongation factor B
V
577Homo sapiensMutation(s): 0 
Gene Names: NELFB (COBRA1, KIAA1182)
Find proteins for Q8WX92 (Homo sapiens)
Go to Gene View: NELFB
Go to UniProtKB:  Q8WX92
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor C/D
W
584Homo sapiensMutation(s): 0 
Gene Names: NELFCD (NELFD, TH1, TH1L)
Find proteins for Q8IXH7 (Homo sapiens)
Go to Gene View: NELFCD
Go to UniProtKB:  Q8IXH7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor E,Negative elongation factor E
X
404Homo sapiensMutation(s): 0 
Gene Names: NELFE (RD, RDBP)
Find proteins for P18615 (Homo sapiens)
Go to Gene View: NELFE
Go to UniProtKB:  P18615
Entity ID: 18
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: 19
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: 20
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: 21
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: 11
MoleculeChainsLengthOrganism
Non-template DNAN48Human immunodeficiency virus 1
Entity ID: 12
MoleculeChainsLengthOrganism
TAR RNAP46Human immunodeficiency virus 1
Entity ID: 13
MoleculeChainsLengthOrganism
Template DNAT48Human immunodeficiency virus 1
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  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
V, W, X
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Experimental preparation
  • Version 2.0: 2019-01-23
    Type: Advisory, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary