5OIK

Structure of an RNA polymerase II-DSIF transcription elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history


Literature

Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.

Bernecky, C.Plitzko, J.M.Cramer, P.

(2017) Nat Struct Mol Biol 24: 809-815

  • DOI: https://doi.org/10.1038/nsmb.3465
  • Primary Citation of Related Structures:  
    5OHO, 5OHQ, 5OIK

  • PubMed Abstract: 

    During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,970Bos taurusMutation(s): 0 
EC: 2.7.7.6
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UniProt GroupG3MZY8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Bos taurusMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Bos taurusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase (RNA) II (DNA directed) polypeptide D142Bos taurusMutation(s): 0 
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UniProt GroupQ1JQ91
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1210Bos taurusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Bos taurusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Bos taurusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein150Bos taurusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Bos taurusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Bos taurusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11117Bos taurusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC458Bos taurusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4P [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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GTEx:  ENSG00000213246 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5Q [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (43-MER)M [auth N]43synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')N [auth P]50synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (43-MER)O [auth T]43synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.10

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860, SPP1935
European Research CouncilGermanyTRANSREGULON
Volkswagen FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Other