2CY7 | pdb_00002cy7

The crystal structure of human Atg4B

• PDB DOI: https://doi.org/10.2210/pdb2CY7/pdb

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


• Deposited: 2005-07-05 Released: 2005-09-13 
• Deposition Author(s): Sugawara, K., Suzuki, N.N., Fujioka, Y., Mizushima, N., Ohsumi, Y., Inagaki, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Structural Basis for the Specificity and Catalysis of Human Atg4B Responsible for Mammalian Autophagy

Sugawara, K., Suzuki, N.N., Fujioka, Y., Mizushima, N., Ohsumi, Y., Inagaki, F.

(2005) J Biological Chem 280: 40058-40065

• PubMed: 16183633 
• DOI: https://doi.org/10.1074/jbc.M509158200
• Primary Citation Related Structures: 
  2CY7


• PubMed Abstract: 
  

  Reversible modification of Atg8 with phosphatidylethanolamine is crucial for autophagy, the bulk degradation system conserved in eukaryotic cells. Atg4 is a novel cysteine protease that processes and deconjugates Atg8. Herein, we report the crystal structure of human Atg4B (HsAtg4B) at 1.9-A resolution. Despite no obvious sequence homology with known proteases, the structure of HsAtg4B shows a classical papain-like fold. In addition to the papain fold region, HsAtg4B has a small alpha/beta-fold domain. This domain is thought to be the binding site for Atg8 homologs. The active site cleft of HsAtg4B is masked by a loop (residues 259-262), implying a conformational change upon substrate binding. The structure and in vitro mutational analyses provide the basis for the specificity and catalysis of HsAtg4B. This will enable the design of Atg4-specific inhibitors that block autophagy.

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Organizational Affiliation: 
• Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.65 kDa 
• Atom Count: 2,817 
• Modeled Residue Count: 333 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine protease APG4B	A	396	Homo sapiens	Mutation(s): 0  EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4P1 (Homo sapiens) Explore Q9Y4P1  Go to UniProtKB:  Q9Y4P1
PHAROS:  Q9Y4P1 GTEx:  ENSG00000168397

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.913	α = 90
b = 88.339	β = 90
c = 160.139	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-13 
Deposition Author(s): Sugawara, K., Suzuki, N.N., Fujioka, Y., Mizushima, N., Ohsumi, Y., Inagaki, F.

Revision History  

• Version 1.0: 2005-09-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references