5OIK

Structure of an RNA polymerase II-DSIF transcription elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 ...

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1
A
1970Bos taurusMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
Find proteins for G3MZY8 (Bos taurus)
Go to Gene View: POLR2A
Go to UniProtKB:  G3MZY8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
B
1174Bos taurusMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for A5PJW8 (Bos taurus)
Go to Gene View: POLR2B
Go to UniProtKB:  A5PJW8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3
C
275Bos taurusMutation(s): 0 
Gene Names: POLR2C
Find proteins for Q3T0Q3 (Bos taurus)
Go to Gene View: POLR2C
Go to UniProtKB:  Q3T0Q3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Polymerase (RNA) II (DNA directed) polypeptide D
D
142Bos taurusMutation(s): 0 
Gene Names: POLR2D
Find proteins for Q1JQ91 (Bos taurus)
Go to Gene View: POLR2D
Go to UniProtKB:  Q1JQ91
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1
E
210Bos taurusMutation(s): 0 
Gene Names: POLR2E
Find proteins for Q2T9T3 (Bos taurus)
Go to Gene View: POLR2E
Go to UniProtKB:  Q2T9T3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F
127Bos taurusMutation(s): 0 
Gene Names: POLR2F
Find proteins for Q32PE0 (Bos taurus)
Go to Gene View: POLR2F
Go to UniProtKB:  Q32PE0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7
G
172Bos taurusMutation(s): 0 
Gene Names: POLR2G
Find proteins for Q5E9B8 (Bos taurus)
Go to Gene View: POLR2G
Go to UniProtKB:  Q5E9B8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
H
150Bos taurusMutation(s): 0 
Gene Names: POLR2H
Find proteins for F2Z4H3 (Bos taurus)
Go to Gene View: POLR2H
Go to UniProtKB:  F2Z4H3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
125Bos taurusMutation(s): 0 
Gene Names: POLR2I
Find proteins for Q32P73 (Bos taurus)
Go to Gene View: POLR2I
Go to UniProtKB:  Q32P73
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J
67Bos taurusMutation(s): 0 
Gene Names: POLR2L
Find proteins for Q32P78 (Bos taurus)
Go to Gene View: POLR2L
Go to UniProtKB:  Q32P78
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11
K
117Bos taurusMutation(s): 0 
Gene Names: POLR2J
Find proteins for Q32P79 (Bos taurus)
Go to Gene View: POLR2J
Go to UniProtKB:  Q32P79
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L
58Bos taurusMutation(s): 0 
Gene Names: POLR2K
Find proteins for Q3ZBC0 (Bos taurus)
Go to Gene View: POLR2K
Go to UniProtKB:  Q3ZBC0
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT4
Y
117Homo 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: 17
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: 13
MoleculeChainsLengthOrganism
DNA (43-MER)N43synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
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')P50synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA (43-MER)T43synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, I, J, L, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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
German Research FoundationGermanySFB860, SPP1935
European Research CouncilGermanyTRANSREGULON
Volkswagen FoundationGermany--

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy