1JUQ

GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


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

Literature

Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains.

Misra, S., Puertollano, R., Kato, Y., Bonifacino, J.S., Hurley, J.H.

(2002) Nature 415: 933-937

  • DOI: 10.1038/415933a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Specific sorting signals direct transmembrane proteins to the compartments of the endosomal-lysosomal system. Acidic-cluster-dileucine signals present within the cytoplasmic tails of sorting receptors, such as the cation-independent and cation-depend ...

    Specific sorting signals direct transmembrane proteins to the compartments of the endosomal-lysosomal system. Acidic-cluster-dileucine signals present within the cytoplasmic tails of sorting receptors, such as the cation-independent and cation-dependent mannose-6-phosphate receptors, are recognized by the GGA (Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding) proteins. The VHS (Vps27p, Hrs and STAM) domains of the GGA proteins are responsible for the highly specific recognition of these acidic-cluster-dileucine signals. Here we report the structures of the VHS domain of human GGA3 complexed with signals from both mannose-6-phosphate receptors. The signals bind in an extended conformation to helices 6 and 8 of the VHS domain. The structures highlight an Asp residue separated by two residues from a dileucine sequence as critical recognition elements. The side chains of the Asp-X-X-Leu-Leu sequence interact with subsites consisting of one electropositive and two shallow hydrophobic pockets, respectively. The rigid spatial alignment of the three binding subsites leads to high specificity.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3
A, B, C, D
171Homo sapiensMutation(s): 0 
Gene Names: GGA3 (KIAA0154)
Find proteins for Q9NZ52 (Homo sapiens)
Go to Gene View: GGA3
Go to UniProtKB:  Q9NZ52
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cation-dependent mannose-6-phosphate receptor
E, F, G, H
13Homo sapiensMutation(s): 0 
Gene Names: M6PR (MPR46, MPRD)
Find proteins for P20645 (Homo sapiens)
Go to Gene View: M6PR
Go to UniProtKB:  P20645
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 123.640α = 90.00
b = 131.350β = 90.00
c = 108.140γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-10-12
    Type: Advisory