1X79

Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


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


Literature

Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5.

Zhu, G., Zhai, P., He, X., Wakeham, N., Rodgers, K., Li, G., Tang, J., Zhang, X.C.

(2004) EMBO J 23: 3909-3917

  • DOI: 10.1038/sj.emboj.7600411
  • Primary Citation of Related Structures:  
    1X79

  • PubMed Abstract: 

    • GGA proteins coordinate the intracellular trafficking of clathrin-coated vesicles through their interaction with several other proteins. The GAT domain of GGA proteins interacts with ARF, ubiquitin, and Rabaptin5. The GGA-Rabaptin5 interaction is believe ...

    GGA proteins coordinate the intracellular trafficking of clathrin-coated vesicles through their interaction with several other proteins. The GAT domain of GGA proteins interacts with ARF, ubiquitin, and Rabaptin5. The GGA-Rabaptin5 interaction is believed to function in the fusion of trans-Golgi-derived vesicles to endosomes. We determined the crystal structure of a human GGA1 GAT domain fragment in complex with the Rabaptin5 GAT-binding domain. In this structure, the Rabaptin5 domain is a 90-residue-long helix. At the N-terminal end, it forms a parallel coiled-coil homodimer, which binds one GAT domain of GGA1. In the C-terminal region, it further assembles into a four-helix bundle tetramer. The Rabaptin5-binding motif of the GGA1 GAT domain consists of a three-helix bundle. Thus, the binding between Rabaptin5 and GGA1 GAT domain is based on a helix bundle-helix bundle interaction. The current structural observation is consistent with previously reported mutagenesis data, and its biological relevance is further confirmed by new mutagenesis studies and affinity analysis. The four-helix bundle structure of Rabaptin5 suggests a functional role in tethering organelles.

    Organizational Affiliation: 

    Crystallography Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosylation factor binding protein GGA1 A98Homo sapiensMutation(s): 0 
Gene Names: GGA1
Find proteins for Q9UJY5 (Homo sapiens)
Explore Q9UJY5 
Go to UniProtKB:  Q9UJY5
NIH Common Fund Data Resources
PHAROS:  Q9UJY5
GTEx:  ENSG00000100083
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rab GTPase binding effector protein 1 B, C112Homo sapiensMutation(s): 0 
Gene Names: RABEP1, RABPT5, RABPT5A, RAB5EP
Find proteins for Q15276 (Homo sapiens)
Explore Q15276 
Go to UniProtKB:  Q15276
NIH Common Fund Data Resources
PHAROS:  Q15276
GTEx:  ENSG00000029725
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT
Download Ideal Coordinates CCD File 
B, C
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.222α = 90
b = 155.222β = 90
c = 53.052γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2004-08-13 
  • Released Date: 2004-10-12 
    • Deposition Author(s): Zhu, G., Zhang, X.C.

Revision History 

  • Version 1.0: 2004-10-12
    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: 2017-12-20
    Changes: Database references