5UBP

TREX2 M-region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex.

Gordon, J.M.B.Aibara, S.Stewart, M.

(2017) Nucleic Acids Res 45: 5577-5585

  • DOI: https://doi.org/10.1093/nar/gkx158
  • Primary Citation of Related Structures:  
    5UBP

  • PubMed Abstract: 

    Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805. Although the M-region of Sac3 was originally thought to encompass residues ∼250-550, we report here the 2.3Å resolution crystal structure of a complex containing Sac3 residues 60-550 that indicates that the TPR-like repeats of the M-region extend to residue 137 and that residues 90-125 form a novel loop that links Sac3 to Thp1. These new structural elements are important for growth and mRNA export in vivo. Although deleting Sac3 residues 1-90 produced a wild-type phenotype, deletion of the loop as well generated growth defects at 37°C, whereas the deletion of residues 1-250 impaired mRNA export and also generated longer lag times when glucose or raffinose was replaced by galactose as the carbon source.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine permease transcriptional regulator482Saccharomyces cerevisiae RM11-1aMutation(s): 0 
Gene Names: SCRG_00364
UniProt
Find proteins for B3LGC5 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LGC5 
Go to UniProtKB:  B3LGC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3LGC5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear mRNA export protein THP1455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: THP1BUD29YOL072WO1140
UniProt
Find proteins for Q08231 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08231 
Go to UniProtKB:  Q08231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08231
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM189Saccharomyces 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94742
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.368α = 90
b = 86.634β = 90
c = 168.338γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105178939

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description