Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.81 kDa 
• Atom Count: 1151 
• Modelled Residue Count: 139 
• Deposited Residue Count: 147 
• Unique protein chains: 1

1JWF

Crystal Structure of human GGA1 VHS domain.

• DOI: 10.2210/pdb1JWF/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-04 Released: 2002-03-06 
• Deposition Author(s): Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.261 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

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

• PubMed: 11859376 
• DOI: 10.1038/415937a
• Primary Citation of Related Structures:  
  1JWG, 1JWF


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor binding protein GGA1	A	147	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.261 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.12	α = 90
b = 55.12	β = 90
c = 105.513	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-04 
• Released Date: 2002-03-06 
Deposition Author(s): Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K., Wakatsuki, S.

Revision History  

• 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: 2018-06-20
  Changes: Data collection, Structure summary