4GWP | pdb_00004gwp

Structure of the Mediator Head Module from S. cerevisiae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 
    0.357 (Depositor), 0.355 (DCC) 
  • R-Value Work: 
    0.290 (Depositor), 0.289 (DCC) 
  • R-Value Observed: 
    0.294 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4GWP

This is version 1.2 of the entry. See complete history. 

Literature

Structure of the Mediator Head module bound to the carboxy-terminal domain of RNA polymerase II.

Robinson, P.J., Bushnell, D.A., Trnka, M.J., Burlingame, A.L., Kornberg, R.D.

(2012) Proc Natl Acad Sci U S A 109: 17931-17935

  • DOI: https://doi.org/10.1073/pnas.1215241109
  • Primary Citation Related Structures: 
    4GWP, 4GWQ

  • PubMed Abstract: 

    The X-ray crystal structure of the Head module, one-third of the Mediator of transcriptional regulation, has been determined as a complex with the C-terminal domain (CTD) of RNA polymerase II. The structure reveals multiple points of interaction with an extended conformation of the CTD; it suggests a basis for regulation by phosphorylation of the CTD. Biochemical studies show a requirement for Mediator-CTD interaction for transcription.

    • Organizational Affiliation: 
    • Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 241.79 kDa 
  • Atom Count: 9,033 
  • Modeled Residue Count: 1,541 
  • Deposited Residue Count: 2,142 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11115Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99278 
Go to UniProtKB:  Q99278
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99278
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17687Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32569 
Go to UniProtKB:  P32569
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32569
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8407Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38304 
Go to UniProtKB:  P38304
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38304
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22121Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32570 
Go to UniProtKB:  P32570
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32570
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18307Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P32585 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32585 
Go to UniProtKB:  P32585
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32585
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20210Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P34162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34162 
Go to UniProtKB:  P34162
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34162
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6295Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38782 
Go to UniProtKB:  P38782
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38782
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free:  0.357 (Depositor), 0.355 (DCC) 
  • R-Value Work:  0.290 (Depositor), 0.289 (DCC) 
  • R-Value Observed: 0.294 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.011α = 90
b = 142.011β = 90
c = 305.345γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references