5NUV | pdb_00005nuv

Structure of the WD40-domain of human ATG16L1

• PDB DOI: https://doi.org/10.2210/pdb5NUV/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2017-05-02 Released: 2017-07-19 
• Deposition Author(s): Bajagic, M., Scrima, A.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structure of the WD40-domain of human ATG16L1.

Bajagic, M., Archna, A., Busing, P., Scrima, A.

(2017) Protein Sci 26: 1828-1837

• PubMed: 28685931 
• DOI: https://doi.org/10.1002/pro.3222
• Primary Citation Related Structures: 
  5NUV


• PubMed Abstract: 
  

  Autophagy-related protein ATG16L1 is a component of the mammalian ATG12∼ATG5/ATG16L1 complex, which acts as E3-ligase to catalyze lipidation of LC3 during autophagosome biogenesis. The N-terminal part of ATG16L1 comprises the ATG5-binding site and coiled-coil dimerization domain, both also present in yeast ATG16 and essential for bulk and starvation induced autophagy. While absent in yeast ATG16, mammalian ATG16L1 further contains a predicted C-terminal WD40-domain, which has been shown to be involved in mediating interaction with diverse factors in the context of alternative functions of autophagy, such as inflammatory control and xenophagy. In this work, we provide detailed information on the domain boundaries of the WD40-domain of human ATG16L1 and present its crystal structure at a resolution of 1.55 Å.

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Organizational Affiliation: 
• Structural Biology of Autophagy Group, Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, 38124, 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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.58 kDa 
• Atom Count: 2,542 
• Modeled Residue Count: 301 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 16-1	A	309	Homo sapiens	Mutation(s): 3  Gene Names: ATG16L1, APG16L, UNQ9393/PRO34307
UniProt & NIH Common Fund Data Resources
Find proteins for Q676U5 (Homo sapiens) Explore Q676U5  Go to UniProtKB:  Q676U5
PHAROS:  Q676U5 GTEx:  ENSG00000085978

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BU3	B [auth A]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.55	α = 90
b = 38.22	β = 105.74
c = 45.62	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Bajagic, M., Scrima, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	VH-NG-727

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description