1NA8 | pdb_00001na8

Crystal structure of ADP-ribosylation factor binding protein GGA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.279 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.219 (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

Binding partners for the COOH-terminal appendage domains of the GGAs and gamma-adaptin

Lui, W.W.Collins, B.M.Hirst, J.Motley, A.Millar, C.Schu, P.Owen, D.J.Robinson, M.S.

(2003) Mol Cell Biol 14: 2385-23898

  • DOI: https://doi.org/10.1091/mbc.e02-11-0735
  • Primary Citation Related Structures: 
    1NA8

  • PubMed Abstract: 

    The adaptor appendage domains are believed to act as binding platforms for coated vesicle accessory proteins. Using glutathione S-transferase pulldowns from pig brain cytosol, we find three proteins that can bind to the appendage domains of both the AP-1 gamma subunit and the GGAs: gamma-synergin and two novel proteins, p56 and p200. p56 elicited better antibodies than p200 and was generally more tractable. Although p56 and gamma-synergin bind to both GGA and gamma appendages in vitro, immunofluorescence labeling of nocodazole-treated cells shows that p56 colocalizes with GGAs on TGN46-positive membranes, whereas gamma-synergin colocalizes with AP-1 primarily on a different membrane compartment. Furthermore, in AP-1-deficient cells, p56 remains membrane-associated whereas gamma-synergin becomes cytosolic. Thus, p56 and gamma-synergin show very strong preferences for GGAs and AP-1, respectively, in vivo. However, the GGA and gamma appendages share the same fold as determined by x-ray crystallography, and mutagenesis reveals that the same amino acids contribute to their binding sites. By overexpressing wild-type GGA and gamma appendage domains in cells, we can drive p56 and gamma-synergin, respectively, into the cytosol, suggesting a possible mechanism for selectively disrupting the two pathways.


  • Organizational Affiliation
    • Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 34.71 kDa 
  • Atom Count: 2,499 
  • Modeled Residue Count: 296 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylation factor binding protein GGA1
A, B
154Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJY5 (Homo sapiens)
Explore Q9UJY5 
Go to UniProtKB:  Q9UJY5
PHAROS:  Q9UJY5
GTEx:  ENSG00000100083 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJY5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.279 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.426α = 90
b = 65.426β = 90
c = 142.725γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2018-02-14
    Changes: Experimental preparation
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description