7L8R

Crystal structure of human GPX4-U46C mutant K48A

• PDB DOI: https://doi.org/10.2210/pdb7L8R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-31 Released: 2021-12-29 
• Deposition Author(s): Forouhar, F., Liu, H., Seibt, T., Saneto, R., Wigby, K., Friedman, J., Xia, X., Shchepinov, M.S., Ramesh, S., Conrad, M., Stockwell, B.R.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Cancer Institute (NIH/NCI), Marie Sklodowska-Curie Actions, FragNET ITN, Ministry of Science and Higher Education of the Russian Federation, European Research Council (ERC), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.177 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Patient-derived variant of GPX4 reveals the structural basis for its catalytic activity and degradation mechanism

Liu, H., Forouhar, F., Seibt, T., Saneto, R., Wigby, K., Friedman, J., Xia, X., Shchepinov, M.S., Ramesh, S., Conrad, M., Stockwell, B.R.

(2021) Nat Chem Biol 

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

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: 43.72 kDa 
• Atom Count: 3,053 
• Modelled Residue Count: 328 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Cytoplasmic of Phospholipid hydroperoxide glutathione peroxidase	A, B	192	Homo sapiens	Mutation(s): 2  Gene Names: GPX4 EC: 1.11.1.12 (PDB Primary Data), 1.11.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens) Explore P36969  Go to UniProtKB:  P36969
PHAROS:  P36969 GTEx:  ENSG00000167468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN (Subject of Investigation/LOI)	C [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.177 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.804	α = 90
b = 68.559	β = 90
c = 81.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-29 
Deposition Author(s): Forouhar, F., Liu, H., Seibt, T., Saneto, R., Wigby, K., Friedman, J., Xia, X., Shchepinov, M.S., Ramesh, S., Conrad, M., Stockwell, B.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R61NS109407
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01CA87497
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35CA209896
Marie Sklodowska-Curie Actions, FragNET ITN	Germany	03VP04260
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2019-1933
European Research Council (ERC)	European Union	GA 884754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R24GM141256
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM124165

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description