1JWG | pdb_00001jwg

VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.261 (Depositor) 
  • R-Value Work: 
    0.226 (Depositor) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1JWG

This is version 1.4 of the entry. See complete history

Literature

Structural basis for recognition of acidic-cluster dileucine sequence by GGA1.

Shiba, T.Takatsu, H.Nogi, T.Matsugaki, N.Kawasaki, M.Igarashi, N.Suzuki, M.Kato, R.Earnest, T.Nakayama, K.Wakatsuki, S.

(2002) Nature 415: 937-941

  • DOI: https://doi.org/10.1038/415937a
  • Primary Citation Related Structures: 
    1JWF, 1JWG

  • PubMed Abstract: 

    GGAs (Golgi-localizing, gamma-adaptin ear homology domain, ARF-interacting proteins) are critical for the transport of soluble proteins from the trans-Golgi network (TGN) to endosomes/lysosomes by means of interactions with TGN-sorting receptors, ADP-ribosylation factor (ARF), and clathrin. The amino-terminal VHS domains of GGAs form complexes with the cytoplasmic domains of sorting receptors by recognizing acidic-cluster dileucine (ACLL) sequences. Here we report the X-ray structure of the GGA1 VHS domain alone, and in complex with the carboxy-terminal peptide of cation-independent mannose 6-phosphate receptor containing an ACLL sequence. The VHS domain forms a super helix with eight alpha-helices, similar to the VHS domains of TOM1 and Hrs. Unidirectional movements of helices alpha6 and alpha8, and some of their side chains, create a set of electrostatic and hydrophobic interactions for correct recognition of the ACLL peptide. This recognition mechanism provides the basis for regulation of protein transport from the TGN to endosomes/lysosomes, which is shared by sortilin and low-density lipoprotein receptor-related protein.


  • Organizational Affiliation
    • Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.

Macromolecule Content 

  • Total Structure Weight: 37.48 kDa 
  • Atom Count: 2,559 
  • Modeled Residue Count: 292 
  • Deposited Residue Count: 320 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylation factor binding protein GGA1A,
C [auth B]
147Homo 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
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cation-independent mannose-6-phosphate receptorB [auth C],
D
13N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P11717 (Homo sapiens)
Explore P11717 
Go to UniProtKB:  P11717
PHAROS:  P11717
GTEx:  ENSG00000197081 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11717
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.261 (Depositor) 
  • R-Value Work:  0.226 (Depositor) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.146α = 90
b = 65.77β = 90
c = 101.426γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary