5CN1 | pdb_00005cn1

Crystal structure of yeast GGA1_GAE domain-P21

• PDB DOI: https://doi.org/10.2210/pdb5CN1/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-17 Released: 2016-07-20 
• Deposition Author(s): Zhang, F., Song, Y., Li, X., Teng, M.K.
• Funding Organization(s): the Chinese Ministry of Science and Technology, the Chinese National Natural Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the accessory protein recruitment by yeast GGA1_GAE domain

Zhang, F., Song, Y., Li, X., Teng, M.K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.19 kDa 
• Atom Count: 3,441 
• Modeled Residue Count: 452 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-binding protein GGA1	A, B, C, D	125	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: GGA1, YDR358W, D9476.2
UniProt
Find proteins for Q06336 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06336  Go to UniProtKB:  Q06336

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.007	α = 90
b = 53.585	β = 103.57
c = 71.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Zhang, F., Song, Y., Li, X., Teng, M.K.

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Funding Organization	Location	Grant Number
the Chinese Ministry of Science and Technology	China	2012CB917200 and 2009CB825500
the Chinese National Natural Science Foundation	China	31270014, 31130018, 30900224 and 10979039

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary