Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 55.09 kDa 
• Atom Count: 3574 
• Modelled Residue Count: 430 
• Deposited Residue Count: 486 
• Unique protein chains: 2

2ZZP

The crystal structure of human Atg4B(C74S)- LC3(1-124) complex

• PDB DOI: 10.2210/pdb2ZZP/pdb

• Classification: HYDROLASE/STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-22 Released: 2009-03-03 
• Deposition Author(s): Satoo, K., Noda, N.N., Inagaki, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.

Satoo, K., Noda, N.N., Kumeta, H., Fujioka, Y., Mizushima, N., Ohsumi, Y., Inagaki, F.

(2009) EMBO J 28: 1341-1350

• PubMed: 19322194 
• DOI: 10.1038/emboj.2009.80
• Primary Citation of Related Structures:  
  2Z0D, 2Z0E, 2ZZP


• PubMed Abstract: 
  

Atg8 is conjugated to phosphatidylethanolamine (PE) by ubiquitin-like conjugation reactions. Atg8 has at least two functions in autophagy: membrane biogenesis and target recognition. Regulation of PE conjugation and deconjugation of Atg8 is crucial for these functions in which Atg4 has a critical function by both processing Atg8 precursors and deconjugating Atg8-PE. Here, we report the crystal structures of catalytically inert human Atg4B (HsAtg4B) in complex with processed and unprocessed forms of LC3, a mammalian orthologue of yeast Atg8. On LC3 binding, the regulatory loop and the N-terminal tail of HsAtg4B undergo large conformational changes. The regulatory loop masking the entrance of the active site of free HsAtg4B is lifted by LC3 Phe119, so that a groove is formed along which the LC3 tail enters the active site. At the same time, the N-terminal tail masking the exit of the active site of HsAtg4B in the free form is detached from the enzyme core and a large flat surface is exposed, which might enable the enzyme to access the membrane-bound LC3-PE.

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Organizational Affiliation: 

Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine protease ATG4B	A	357	Homo sapiens	Mutation(s): 1  Gene Names: ATG4B, APG4B, AUTL1, KIAA0943 EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4P1 (Homo sapiens) Explore Q9Y4P1  Go to UniProtKB:  Q9Y4P1
PHAROS:  Q9Y4P1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated proteins 1A/1B light chain 3B	B	129	Rattus norvegicus	Mutation(s): 0  Gene Names: Map1lc3b, Map1alc3, Map1lc3
UniProt
Find proteins for Q62625 (Rattus norvegicus) Explore Q62625  Go to UniProtKB:  Q62625

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.25	α = 90
b = 93.146	β = 90
c = 101.999	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-22 
• Released Date: 2009-03-03 
Deposition Author(s): Satoo, K., Noda, N.N., Inagaki, F.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references