4TRQ

Crystal structure of Sac3/Thp1/Sem1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression.

Schneider, M.Hellerschmied, D.Schubert, T.Amlacher, S.Vinayachandran, V.Reja, R.Pugh, B.F.Clausen, T.Kohler, A.

(2015) Cell 162: 1016-1028

  • DOI: 10.1016/j.cell.2015.07.059
  • Primary Citation of Related Structures:  
    4TRQ

  • PubMed Abstract: 
  • Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown ...

    Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with the Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent at specific genes. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing. Our data provide mechanistic insight into how an NPC-associated adaptor complex accesses the core transcription machinery.


    Organizational Affiliation

    Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria. Electronic address: alwin.koehler@mfpl.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear mRNA export protein SAC3A, D299Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAC3LEP1YDR159WYD8358.13
UniProt
Find proteins for P46674 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46674 
Go to UniProtKB:  P46674
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear mRNA export protein THP1B, E286Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: THP1BUD29YOL072WO1140
UniProt
Find proteins for Q08231 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08231 
Go to UniProtKB:  Q08231
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1C, F60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEM1DSH1YDR363W-A
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O94742 
Go to UniProtKB:  O94742
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.741α = 90
b = 125.741β = 90
c = 268.367γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Omodel building
PHENIXrefinement
XSCALEdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references