3C0T | pdb_00003c0t

Structure of the Schizosaccharomyces pombe Mediator subcomplex Med8C/18

• PDB DOI: https://doi.org/10.2210/pdb3C0T/pdb

• Classification: TRANSCRIPTION
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-21 Released: 2008-04-22 
• Deposition Author(s): Lariviere, L., Seizl, M., van Wageningen, S., Roether, S., van de Pasch, L., Feldmann, H., Straesser, K., Hahn, S., Holstege, C.P., Cramer, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 

Starting Model: other

Literature

Structure-system correlation identifies a gene regulatory Mediator submodule

Lariviere, L., Seizl, M., van Wageningen, S., Rother, S., van de Pasch, L., Feldmann, H., Strasser, K., Hahn, S., Holstege, F.C.P., Cramer, P.

(2008) Genes Dev 22: 872-877

• PubMed: 18381891 
• DOI: https://doi.org/10.1101/gad.465108
• Primary Citation Related Structures: 
  3C0T


• PubMed Abstract: 
  

  A combination of crystallography, biochemistry, and gene expression analysis identifies the coactivator subcomplex Med8C/18/20 as a functionally distinct submodule of the Mediator head module. Med8C forms a conserved alpha-helix that tethers Med18/20 to the Mediator. Deletion of Med8C in vivo results in dissociation of Med18/20 from Mediator and in loss of transcription activity of extracts. Deletion of med8C, med18, or med20 causes similar changes in the yeast transcriptome, establishing Med8C/18/20 as a predominantly positive, gene-specific submodule required for low transcription levels of nonactivated genes, including conjugation genes. The presented structure-based system perturbation is superior to gene deletion analysis of gene regulation.

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Organizational Affiliation: 
• Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.92 kDa 
• Atom Count: 1,884 
• Modeled Residue Count: 224 
• Deposited Residue Count: 240 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 18	A	207	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: med18
UniProt
Find proteins for O14198 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O14198  Go to UniProtKB:  O14198

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 8	B	33	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: med8
UniProt
Find proteins for O94646 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O94646  Go to UniProtKB:  O94646

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.016	α = 90
b = 111.016	β = 90
c = 68.64	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Lariviere, L., Seizl, M., van Wageningen, S., Roether, S., van de Pasch, L., Feldmann, H., Straesser, K., Hahn, S., Holstege, C.P., Cramer, P.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description