2VYI | pdb_00002vyi

Crystal Structure of the TPR domain of Human SGT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural and Functional Characterization of Human Sgt and its Interaction with Vpu of the Human Immunodeficiency Virus Type 1.

Dutta, S.Tan, Y.J.

(2008) Biochemistry 47: 10123

  • DOI: https://doi.org/10.1021/bi800758a
  • Primary Citation Related Structures: 
    2VYI

  • PubMed Abstract: 

    The small glutamine-rich tetratricopeptide repeat protein (SGT) belongs to a family of cochaperones that interacts with both Hsp70 and Hsp90 via the so-called TPR domain. Here, we present the crystal structure of the TPR domain of human SGT (SGT-TPR), which shows that it contains typical features found in the structures of other TPR domains. Previous studies show that full-length SGT can bind to both Vpu and Gag of human immunodeficiency virus type 1 (HIV-1) and the overexpression of SGT in cells reduces the efficiency of HIV-1 particle release. We show that SGT-TPR can bind Vpu and reduce the amount of HIV-1 p24, which is the viral capsid, secreted from cells transfected with the HIV-1 proviral construct, albeit at a lower efficiency than full-length SGT. This indicates that the TPR domain of SGT is sufficient for the inhibition of HIV-1 particle release but the N- and/or C-terminus also have some contributions. The SGT binding site in Vpu was also identified by using peptide array and confirmed by GST pull-down assay.


  • Organizational Affiliation
    • Collaborative Antiviral Research Group, Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673.

Macromolecule Content 

  • Total Structure Weight: 28.86 kDa 
  • Atom Count: 2,137 
  • Modeled Residue Count: 252 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SGTA PROTEIN
A, B
131Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43765 (Homo sapiens)
Explore O43765 
Go to UniProtKB:  O43765
GTEx:  ENSG00000104969 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43765
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.823α = 90
b = 81.939β = 90
c = 55.923γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary