1YD8

COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, {gamma}-ear-containing, ADP-ribosylation-factor-binding proteins

Prag, G.Lee, S.Mattera, R.Arighi, C.N.Beach, B.M.Bonifacino, J.S.Hurley, J.H.

(2005) Proc Natl Acad Sci U S A 102: 2334-2339

  • DOI: https://doi.org/10.1073/pnas.0500118102
  • Primary Citation of Related Structures:  
    1YD8

  • PubMed Abstract: 

    The Golgi-localized, gamma-ear-containing, Arf (ADP-ribosylation factor)-binding (GGA) proteins are clathrin adaptors that mediate the sorting of transmembrane-cargo molecules at the trans-Golgi network and endosomes. Cargo proteins can be directed into the GGA pathway by at least two different types of sorting signals: acidic cluster-dileucine motifs and covalent modification by ubiquitin. The latter modification is recognized by the GGAs through binding to their GAT [GGA and TOM (target of Myb)] domain. Here we report the crystal structure of the GAT domain of human GGA3 in a 1:1 complex with ubiquitin at 2.8-A resolution. Ubiquitin binds to a hydrophobic and acidic patch on helices alpha1 and alpha2 of the GAT three-helix bundle that includes Asn-223, Leu-227, Glu-230, Met-231, Asp-244, Glu-246, Leu-247, Glu-250, and Leu-251. The GAT-binding surface on ubiquitin is a hydrophobic patch centered on Ile-44 that is also responsible for binding most other ubiquitin effectors. The ubiquitin-binding site observed in the crystal is distinct from the Rabaptin-5-binding site on helices alpha2 and alpha3 of the GAT domain. Mutational analysis and modeling of the ubiquitin-Rabaptin-5-GAT ternary complex indicates that ubiquitin and Rabaptin-5 can bind to the GAT domain at two different sites without any steric conflict. This ability highlights the GAT domain as a hub for interactions with multiple partners in trafficking.


  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINA [auth U],
C [auth V]
76Bos taurusMutation(s): 0 
UniProt
Find proteins for P0CH28 (Bos taurus)
Explore P0CH28 
Go to UniProtKB:  P0CH28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CH28
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3B [auth G],
D [auth H]
98Homo sapiensMutation(s): 0 
Gene Names: GGA3KIAA0154
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ52 (Homo sapiens)
Explore Q9NZ52 
Go to UniProtKB:  Q9NZ52
PHAROS:  Q9NZ52
GTEx:  ENSG00000125447 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ52
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.886α = 90
b = 97.293β = 90.03
c = 66.459γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
COMOphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references
  • Version 1.5: 2024-04-03
    Changes: Refinement description