5GU5

Crystal structure of p24gamma2 GOLD domain determined by sulfur-SAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic analysis of murine p24 gamma 2 Golgi dynamics domain

Nagae, M.Liebschner, D.Yamada, Y.Morita-Matsumoto, K.Matsugaki, N.Senda, T.Fujita, M.Kinoshita, T.Yamaguchi, Y.

(2017) Proteins 85: 764-770

  • DOI: 10.1002/prot.25242

  • PubMed Abstract: 
  • The p24 family proteins form homo- and hetero-oligomeric complexes for efficient transport of cargo proteins from the endoplasmic reticulum to the Golgi apparatus. It consists of four subfamilies (p24α, p24β, p24γ, and p24δ). p24γ2 plays crucial role ...

    The p24 family proteins form homo- and hetero-oligomeric complexes for efficient transport of cargo proteins from the endoplasmic reticulum to the Golgi apparatus. It consists of four subfamilies (p24α, p24β, p24γ, and p24δ). p24γ2 plays crucial roles in the selective transport of glycosylphosphatidylinositol-anchored proteins. Here, we determined the crystal structure of mouse p24γ2 Golgi dynamics (GOLD) domain at 2.8 Å resolution by the single anomalous diffraction method using intrinsic sulfur atoms. In spite of low sequence identity among p24 family proteins, p24γ2 GOLD domain assumes a β-sandwich fold, similar to that of p24β1 or p24δ1. An additional short α-helix is observed at the C-terminus of the p24γ2 GOLD domain. Intriguingly, p24γ2 GOLD domains crystallize as dimers, and dimer formation seems assisted by the short α-helix. Dimerization modes of GOLD domains are compared among p24 family proteins. Proteins 2017; 85:764-770. © 2016 Wiley Periodicals, Inc.


    Organizational Affiliation

    Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako-City, Saitama, 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transmembrane emp24 domain-containing protein 5
A
114Mus musculusMutation(s): 0 
Gene Names: Tmed5
Find proteins for Q9CXE7 (Mus musculus)
Go to UniProtKB:  Q9CXE7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.224 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.410α = 90.00
b = 79.410β = 90.00
c = 125.948γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Takeda Science FoundationJapan--
MEXTJapan25121738

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references