5NUV

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.197
R-Value Work: 0.165
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.3222
Primary Citation of 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.

Organizational Affiliation

Structural Biology of Autophagy Group, Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q676U5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU3 Query on BU3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.197
R-Value Work: 0.165
R-Value Observed: 0.167
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Bajagic, M.

Scrima, A.

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

Revision History (Full details and data files)

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