3M95 | pdb_00003m95

Crystal structure of autophagy-related protein Atg8 from the silkworm Bombyx mori

• PDB DOI: https://doi.org/10.2210/pdb3M95/pdb

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


• Deposited: 2010-03-20 Released: 2010-07-21 
• Deposition Author(s): Teng, Y.-B., Hu, C., Zhang, X., Jiang, Y.L., Hu, H.-X., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structure of autophagy-related protein Atg8 from the silkworm Bombyx mori

Hu, C., Zhang, X., Teng, Y.-B., Hu, H.-X., Li, W.-F.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 787-790

• PubMed: 20606273 
• DOI: https://doi.org/10.1107/S1744309110018464
• Primary Citation of Related Structures:  
  3M95


• PubMed Abstract: 
  

  Autophagy-related protein Atg8 is ubiquitous in all eukaryotes. It is involved in the Atg8-PE ubiquitin-like conjugation system, which is essential for autophagosome formation. The structures of Atg8 from different species are very similar and share a ubiquitin-fold domain at the C-terminus. In the 2.40 A crystal structure of Atg8 from the silkworm Bombyx mori reported here, the ubiquitin fold at the C-terminus is preceded by two additional helices at the N-terminus.

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, People's Republic of China.

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: 29.89 kDa 
• Atom Count: 2,009 
• Modeled Residue Count: 231 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy related protein Atg8	A, B	125	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for Q2F5R5 (Bombyx mori) Explore Q2F5R5  Go to UniProtKB:  Q2F5R5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.768	α = 90
b = 96.768	β = 90
c = 44.309	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Teng, Y.-B., Hu, C., Zhang, X., Jiang, Y.L., Hu, H.-X., Zhou, C.Z.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description