4NAW

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12.

Metlagel, Z.Otomo, C.Takaesu, G.Otomo, T.

(2013) Proc Natl Acad Sci U S A 110: 18844-18849

  • DOI: 10.1073/pnas.1314755110
  • Primary Citation of Related Structures:  
    4NAW

  • PubMed Abstract: 
  • The autophagic ubiquitin-like protein (ublp) autophagy-related (ATG)12 is a component of the ATG12∼ATG5-ATG16L1 E3 complex that promotes lipid conjugation of members of the LC3 ublp family. A role of ATG12 in the E3 complex is to recruit the E2 enzym ...

    The autophagic ubiquitin-like protein (ublp) autophagy-related (ATG)12 is a component of the ATG12∼ATG5-ATG16L1 E3 complex that promotes lipid conjugation of members of the LC3 ublp family. A role of ATG12 in the E3 complex is to recruit the E2 enzyme ATG3. Here we report the identification of the ATG12 binding sequence in the flexible region of human ATG3 and the crystal structure of the minimal E3 complexed with the identified binding fragment of ATG3. The structure shows that 13 residues of the ATG3 fragment form a short β-strand followed by an α-helix on a surface area that is exclusive to ATG12. Mutational analyses of ATG3 confirm that four residues whose side chains make contacts with ATG12 are important for E3 interaction as well as LC3 lipidation. Conservation of these four critical residues is high in metazoan organisms and plants but lower in fungi. A structural comparison reveals that the ATG3 binding surface on ATG12 contains a hydrophobic pocket corresponding to the binding pocket of LC3 that accommodates the leucine of the LC3-interacting region motif. These findings establish the mechanism of ATG3 recruitment by ATG12 in higher eukaryotes and place ATG12 among the members of signaling ublps that bind liner sequences.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.



Macromolecules
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like-conjugating enzyme ATG3DHLP34Homo sapiensMutation(s): 0 
Gene Names: APG3APG3LATG3
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for Q9NT62 (Homo sapiens)
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Go to UniProtKB:  Q9NT62
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PHAROS  Q9NT62
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein ATG12AEIM91Homo sapiensMutation(s): 0 
Gene Names: APG12APG12LATG12
Find proteins for O94817 (Homo sapiens)
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Go to UniProtKB:  O94817
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PHAROS  O94817
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Autophagy protein 5BFJN275Homo sapiensMutation(s): 0 
Gene Names: APG5LASPATG5
Find proteins for Q9H1Y0 (Homo sapiens)
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Go to UniProtKB:  Q9H1Y0
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PHAROS  Q9H1Y0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Autophagy-related protein 16-1CGKO36Homo sapiensMutation(s): 0 
Gene Names: APG16LATG16L1UNQ9393/PRO34307
Find proteins for Q676U5 (Homo sapiens)
Explore Q676U5 
Go to UniProtKB:  Q676U5
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PHAROS  Q676U5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B, F, J, N
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download CCD File 
B, F, J, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.584α = 90
b = 120.097β = 90
c = 189.466γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2013-12-18
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description