4CO7

Crystal structure of human GATE-16

• PDB DOI: https://doi.org/10.2210/pdb4CO7/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-27 Released: 2015-01-14 
• Deposition Author(s): Weiergraeber, O.H., Ma, P., Willbold, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.188 

Literature

Conformational Polymorphism in Autophagy-Related Protein Gate-16.

Ma, P., Schillinger, O., Schwarten, M., Lecher, J., Hartmann, R., Stoldt, M., Mohrluder, J., Olubiyi, O., Strodel, B., Willbold, D., Weiergraber, O.H.

(2015) Biochemistry 54: 5469

• PubMed: 26284781 
• DOI: https://doi.org/10.1021/acs.biochem.5b00366
• Primary Citation of Related Structures:  
  4CO7


• PubMed Abstract: 
  

  Autophagy is a fundamental homeostatic process in eukaryotic organisms, fulfilling essential roles in development and adaptation to stress. Among other factors, formation of autophagosomes critically depends on proteins of the Atg8 (autophagy-related protein 8) family, which are reversibly conjugated to membrane lipids. We have applied X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics simulations to study the conformational dynamics of Atg8-type proteins, using GATE-16 (Golgi-associated ATPase enhancer of 16 kDa), also known as GABARAPL2, as a model system. This combination of complementary approaches provides new insight into a structural transition centered on the C-terminus, which is crucial for the biological activity of these proteins.

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Organizational Affiliation: 

Institute of Complex Systems, ICS-6 (Structural Biochemistry), Forschungszentrum Jülich , 52425 Jülich, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.66 kDa 
• Atom Count: 2,073 
• Modelled Residue Count: 236 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2	A, B	119	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60520 (Homo sapiens) Explore P60520  Go to UniProtKB:  P60520
PHAROS:  P60520 GTEx:  ENSG00000034713

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.73	α = 90
b = 67.44	β = 90
c = 58.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data scaling
MOLREP	phasing

Structure Validation

Currently 4CO7 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Weiergraeber, O.H., Ma, P., Willbold, D.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description