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 

wwPDB Validation   3D Report Full Report


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

  • 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 ...

    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1970Bos taurusMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
UniProt
Find proteins for G3MZY8 (Bos taurus)
Explore G3MZY8 
Go to UniProtKB:  G3MZY8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1174Bos taurusMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
UniProt
Find proteins for A5PJW8 (Bos taurus)
Explore A5PJW8 
Go to UniProtKB:  A5PJW8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C275Bos taurusMutation(s): 0 
Gene Names: POLR2C
UniProt
Find proteins for Q3T0Q3 (Bos taurus)
Explore Q3T0Q3 
Go to UniProtKB:  Q3T0Q3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase (RNA) II (DNA directed) polypeptide DD142Bos taurusMutation(s): 0 
Gene Names: POLR2D
UniProt
Find proteins for Q1JQ91 (Bos taurus)
Explore Q1JQ91 
Go to UniProtKB:  Q1JQ91
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E210Bos taurusMutation(s): 0 
Gene Names: POLR2E
UniProt
Find proteins for Q2T9T3 (Bos taurus)
Explore Q2T9T3 
Go to UniProtKB:  Q2T9T3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F127Bos taurusMutation(s): 0 
Gene Names: POLR2F
UniProt
Find proteins for Q32PE0 (Bos taurus)
Explore Q32PE0 
Go to UniProtKB:  Q32PE0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G172Bos taurusMutation(s): 0 
Gene Names: POLR2G
UniProt
Find proteins for Q5E9B8 (Bos taurus)
Explore Q5E9B8 
Go to UniProtKB:  Q5E9B8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinH150Bos taurusMutation(s): 0 
Gene Names: POLR2H
UniProt
Find proteins for F2Z4H3 (Bos taurus)
Explore F2Z4H3 
Go to UniProtKB:  F2Z4H3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I125Bos taurusMutation(s): 0 
Gene Names: POLR2I
UniProt
Find proteins for Q32P73 (Bos taurus)
Explore Q32P73 
Go to UniProtKB:  Q32P73
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J67Bos taurusMutation(s): 0 
Gene Names: POLR2L
UniProt
Find proteins for Q32P78 (Bos taurus)
Explore Q32P78 
Go to UniProtKB:  Q32P78
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K117Bos taurusMutation(s): 0 
Gene Names: POLR2J
UniProt
Find proteins for Q32P79 (Bos taurus)
Explore Q32P79 
Go to UniProtKB:  Q32P79
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L58Bos taurusMutation(s): 0 
Gene Names: POLR2K
UniProt
Find proteins for Q3ZBC0 (Bos taurus)
Explore Q3ZBC0 
Go to UniProtKB:  Q3ZBC0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT4P [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
UniProt & NIH Common Fund Data Resources
Find proteins for P63272 (Homo sapiens)
Explore P63272 
Go to UniProtKB:  P63272
PHAROS:  P63272
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT5Q [auth Z]1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens)
Explore O00267 
Go to UniProtKB:  O00267
PHAROS:  O00267
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsLengthOrganismImage
DNA (43-MER)M [auth N]43synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsLengthOrganismImage
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
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsLengthOrganismImage
DNA (43-MER)O [auth T]43synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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