5L3T

Structure of the Saccharomyces cerevisiae TREX-2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.93 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.338 
  • R-Value Observed: 0.340 

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This is version 1.4 of the entry. See complete history


Literature

The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region.

Aibara, S.Bai, X.C.Stewart, M.

(2016) J Struct Biol 195: 316-324

  • DOI: https://doi.org/10.1016/j.jsb.2016.07.007
  • Primary Citation of Related Structures:  
    5G5P, 5L3T

  • PubMed Abstract: 

    Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export-competent mRNPs through interactions with the general mRNA nuclear export factor Mex67:Mtr2. The TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31, and Sus1 bind. TREX-2 can be subdivided into two modules: one, in which Thp1 and Sem1 bind to the Sac3(M) region (residues ∼100-551), and the other in which Cdc31 and two Sus1 chains bind to the Sac3(CID) region (residues ∼710-805). Complementary structural analyses using X-ray crystallography, electron microscopy, and small-angle X-ray scattering of the Saccharomyces cerevisiae TREX-2 complex, expressed using Baculovirus-infected Sf9 cells, have indicated that the TPR-like repeats of the Sac3(M) region extend considerably further towards the N-terminus than previously thought, and also indicate that this region and Sac3(CID):Sus1:Cdc31 region of the S. cerevisiae complex are structurally independent. Although the density visible accounted for only ∼100kDa, a 5.3Å resolution cryo-EM reconstruction was obtained of the M-region of TREX-2 that showed an additional three putative α-helices extending towards the Sac3 N-terminus and these helices were also seen in a 4.9Å resolution structure obtained by X-ray crystallography.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear mRNA export protein SAC31,301Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SAC3LEP1YDR159WYD8358.13
UniProt
Find proteins for P46674 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P46674
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UniProt GroupP46674
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear mRNA export protein THP1455Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: THP1BUD29YOL072WO1140
UniProt
Find proteins for Q08231 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q08231
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UniProt GroupQ08231
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM189Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEM1DSH1YDR363W-A
UniProt
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O94742 
Go to UniProtKB:  O94742
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UniProt GroupO94742
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Sac3polyAla
D, E
24Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Sac3polyAla12Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.93 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.338 
  • R-Value Observed: 0.340 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.17α = 90
b = 84.09β = 90
c = 165.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2019-10-16
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description