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 

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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 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 ...

    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 subunitA1,970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1,174Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
UniProt
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
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit ED [auth E]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
UniProt
Find proteins for I3LSI7 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit FE [auth F]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinH [auth J]67Sus scrofaMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinI [auth K]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinJ [auth L]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor AN [auth U]528Homo sapiensMutation(s): 0 
Gene Names: NELFA, WHSC2, P/OKcl.15
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor B,Negative elongation factor BO [auth V]577Homo sapiensMutation(s): 0 
Gene Names: NELFB, COBRA1, KIAA1182
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Negative elongation factor C/DP [auth W]584Homo sapiensMutation(s): 0 
Gene Names: NELFCD, NELFD, TH1, TH1L, HSPC130
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Entity ID: 17
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Negative elongation factor E,Negative elongation factor EQ [auth X]404Homo sapiensMutation(s): 0 
Gene Names: NELFE, RD, RDBP
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT4R [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1, SPT4H, SUPT4H
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Entity ID: 19
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Transcription elongation factor SPT5S [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit DT [auth D]142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
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Find proteins for A0A287ADR4 (Sus scrofa)
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Entity ID: 21
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RNA polymerase II subunit GU [auth G]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Find proteins for I3LJZ9 (Sus scrofa)
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Entity ID: 11
MoleculeChainsLengthOrganismImage
Non-template DNAK [auth N]48Human immunodeficiency virus 1
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Entity ID: 12
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TAR RNAL [auth P]46Human immunodeficiency virus 1
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Entity ID: 13
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Template DNAM [auth T]48Human immunodeficiency virus 1
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 Molecular Biology OrganizationGermanyALTF-725-2014
German Research FoundationGermanyDFG SFB860
European Research CouncilGermany693023

Revision History  (Full details and data files)

  • 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