3LDZ

Crystal structure of human STAM1 VHS domain in complex with ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

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This is version 1.3 of the entry. See complete history. 


Literature

VHS domains of ESCRT-0 cooperate in high-avidity binding to polyubiquitinated cargo.

Ren, X., Hurley, J.H.

(2010) EMBO J 29: 1045-1054

  • DOI: 10.1038/emboj.2010.6
  • Primary Citation of Related Structures:  
    3LDZ

  • PubMed Abstract: 

    • VHS (Vps27, Hrs, and STAM) domains occur in ESCRT-0 subunits Hrs and STAM, GGA adapters, and other trafficking proteins. The structure of the STAM VHS domain-ubiquitin complex was solved at 2.6 A resolution, revealing that determinants for ubiquitin recognition are conserved in nearly all VHS domains ...

    VHS (Vps27, Hrs, and STAM) domains occur in ESCRT-0 subunits Hrs and STAM, GGA adapters, and other trafficking proteins. The structure of the STAM VHS domain-ubiquitin complex was solved at 2.6 A resolution, revealing that determinants for ubiquitin recognition are conserved in nearly all VHS domains. VHS domains from all classes of VHS-domain containing proteins in yeast and humans, including both subunits of ESCRT-0, bound ubiquitin in vitro. ESCRTs have been implicated in the sorting of Lys63-linked polyubiquitinated cargo. Intact human ESCRT-0 binds Lys63-linked tetraubiquitin 50-fold more tightly than monoubiquitin, though only 2-fold more tightly than Lys48-linked tetraubiquitin. The gain in affinity is attributed to the cooperation of flexibly connected VHS and UIM motifs of ESCRT-0 in avid binding to the polyubiquitin chain. Mutational analysis of all the five ubiquitin-binding sites in yeast ESCRT-0 shows that cooperation between them is required for the sorting of the Lys63-linked polyubiquitinated cargo Cps1 to the vacuole.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinF [auth E], A [auth F], G73Bos taurusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Signal transducing adapter molecule 1B [auth A], D [auth B], E [auth C], C [auth D]140Homo sapiensMutation(s): 0 
Gene Names: STAM, STAM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92783 (Homo sapiens)
Explore Q92783 
Go to UniProtKB:  Q92783
PHAROS:  Q92783
GTEx:  ENSG00000136738
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.61α = 90
b = 112.13β = 99.43
c = 68.66γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2010-01-13 
  • Released Date: 2010-03-02 
    • Deposition Author(s): Ren, X., Hurley, J.H.

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-02-28
    Changes: Data collection