4WZG | pdb_00004wzg

Structure of human ATG101

• PDB DOI: https://doi.org/10.2210/pdb4WZG/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-19 Released: 2015-06-17 
• Deposition Author(s): Michel, M., Weiergraeber, O.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

The mammalian autophagy initiator complex contains 2 HORMA domain proteins.

Michel, M., Schwarten, M., Decker, C., Nagel-Steger, L., Willbold, D., Weiergraber, O.H.

(2015) Autophagy 11: 2300-2308

• PubMed: 26236954 
• DOI: https://doi.org/10.1080/15548627.2015.1076605
• Primary Citation Related Structures: 
  4WZG


• PubMed Abstract: 
  

  ATG101 is an essential component of the ULK complex responsible for initiating cellular autophagy in mammalian cells; its 3-dimensional structure and molecular function, however, are currently unclear. Here we present the X-ray structure of human ATG101. The protein displays an open HORMA domain fold. Both structural properties and biophysical evidence indicate that ATG101 is locked in this conformation, in contrast to the prototypical HORMA domain protein MAD2. Moreover, we discuss a potential mode of dimerization with ATG13 as a fundamental aspect of ATG101 function.

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Organizational Affiliation: 
• a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich; Jülich , Germany.
b Institut für Physikalische Biologie und BMFZ; Heinrich-Heine-Universität Düsseldorf ; Düsseldorf , Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.11 kDa 
• Atom Count: 1,632 
• Modeled Residue Count: 210 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 101	A	218	Homo sapiens	Mutation(s): 0  Gene Names: ATG101, C12orf44, PP894
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSB4 (Homo sapiens) Explore Q9BSB4  Go to UniProtKB:  Q9BSB4
PHAROS:  Q9BSB4 GTEx:  ENSG00000123395

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.15	α = 90
b = 42.62	β = 97.31
c = 67.21	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Michel, M., Weiergraeber, O.H.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Database references
• Version 1.2: 2016-01-13
  Changes: Database references
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations