3MNM | pdb_00003mnm

Crystal structure of GAE domain of GGA2p from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.229 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the specificity of the GAE domain of yGGA2 for its accessory proteins Ent3 and Ent5

Fang, P.Li, X.Wang, J.Niu, L.Teng, M.

(2010) Biochemistry 49: 7949-7955

  • DOI: https://doi.org/10.1021/bi1010255
  • Primary Citation of Related Structures:  
    3MNM

  • PubMed Abstract: 

    Different assemblies of accessory proteins with clathrin are critical for transporting precisely various cargos between intracellular compartments. GGA proteins are adaptors for clathrin-mediated intracellular trafficking, connecting other accessory and cargo proteins to clathrin-coated vesicles. Both binding to the GAE domain of GGA protein yGGA2 in Saccharomyces cerevisia, Ent3 and Ent5 are involved in different trafficking pathways. Ent5 is ubiquitous and localized in a manner independent of yGGA2, and Ent3 functions preferentially through yGGA2. Not known are the sources of these differences. Here we show not all acidic-phenylalanine motifs in Ent3/5 are active for yGGA2_GAE domain binding. Two of the three acidic-phenylalanine motifs from Ent3 can bind to the yGGA2_GAE domain, while only one of the two motifs from Ent5 can bind. We also determined the crystal structure of the yGGA2_GAE domain at 1.8 A resolution. Structural docking and mutagenesis analysis shows inactive motifs in Ent3 and Ent5 repel yGGA2_GAE binding through disfavored residues at positions 1 and 3. These results suggest accessory proteins may fine-tune the GGA adaptor dependence by adjusting their non-acidic-phenylalanine residues, thus contributing to the distinct role of Ent3 and Ent5 in trafficking.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui 230026, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor-binding protein GGA2
A, B, C
123Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GGA2
UniProt
Find proteins for P38817 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38817 
Go to UniProtKB:  P38817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.229 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.716α = 90
b = 89.716β = 90
c = 117.029γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-03-05
    Changes: Database references
  • Version 1.3: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary