1JPL

GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3A, B, C, D171Homo sapiensMutation(s): 4 
Gene Names: GGA3KIAA0154
Find proteins for Q9NZ52 (Homo sapiens)
Explore Q9NZ52 
Go to UniProtKB:  Q9NZ52
NIH Common Fund Data Resources
PHAROS  Q9NZ52
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cation-Independent Mannose 6-phosphate receptorE, F, G, H12N/AMutation(s): 0 
Find proteins for P11717 (Homo sapiens)
Explore P11717 
Go to UniProtKB:  P11717
NIH Common Fund Data Resources
PHAROS  P11717
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.3α = 90
b = 125.3β = 90
c = 64.6γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
RESOLVEmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance