6GML

Structure of paused transcription complex Pol II-DSIF-NELF

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.1 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
  • Primary Citation of Related Structures:  
    6GML

  • 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. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitA1970Sus 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 LengthOrganismDetailsImage
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 LengthOrganismDetailsImage
RNA polymerase II subunit CC271Sus scrofaMutation(s): 0 
Gene Names: POLR2C
Find proteins for I3LCH3 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit EE210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
Find proteins for I3LSI7 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit FF127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinJ67Sus scrofaMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinK117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinL58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
Find proteins for I3LN51 (Sus scrofa)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor AU528Homo sapiensMutation(s): 0 
Gene Names: NELFA, WHSC2, P/OKcl.15
Find proteins for Q9H3P2 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  Q9H3P2
GTEx  ENSG00000185049
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor B,Negative elongation factor BV577Homo sapiensMutation(s): 0 
Gene Names: NELFB, COBRA1, KIAA1182
Find proteins for Q8WX92 (Homo sapiens)
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PHAROS  Q8WX92
GTEx  ENSG00000188986
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor C/DW584Homo sapiensMutation(s): 0 
Gene Names: NELFCD, NELFD, TH1, TH1L, HSPC130
Find proteins for Q8IXH7 (Homo sapiens)
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PHAROS  Q8IXH7
GTEx  ENSG00000101158
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor E,Negative elongation factor EX404Homo sapiensMutation(s): 0 
Gene Names: NELFE, RD, RDBP
Find proteins for P18615 (Homo sapiens)
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PHAROS  P18615
GTEx  ENSG00000204356
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Y121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1, SPT4H, SUPT4H
Find proteins for P63272 (Homo sapiens)
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PHAROS  P63272
GTEx  ENSG00000213246
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT5Z1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
Find proteins for O00267 (Homo sapiens)
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PHAROS  O00267
GTEx  ENSG00000196235
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit DD142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
Find proteins for A0A287ADR4 (Sus scrofa)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit GG172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa)
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Entity ID: 12
MoleculeChainsLengthOrganismImage
TAR RNAP46Human immunodeficiency virus 1
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Entity ID: 13
MoleculeChainsLengthOrganismImage
Template DNAT48Human immunodeficiency virus 1
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Entity ID: 11
MoleculeChainsLengthOrganismImage
Non-template DNAN48Human immunodeficiency virus 1
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2019-01-23
    Changes: Advisory, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Other