8Q8N | pdb_00008q8n

Crystal structure of human GPX4-U46C-I129S-L130S

• PDB DOI: https://doi.org/10.2210/pdb8Q8N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-18 Released: 2024-08-28 
• Deposition Author(s): Bostock, M.J., Mourao, A., Napolitano, V., Sattler, M., Conrad, M., Popowicz, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.292 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

An ultra-rare variant of GPX4 reveals the structural basis to avert neurodegeneration

Lorenz, S.M., Wahida, A., Elmer, D., Bostock, M.J., Seibt, T., Mourao, A., Trumbach, D., Rizzollo, F., Napolitano, V., Kolonko-Adamska, M., Sommer, J., Woo, M.S., Rothammer, N., Gaussman, S., Alves, F., Burkle, E., Wanninger, J., Boxleitner, K.M., Stadler, M., Doll, S., Mishima, E., Nakamura, T., Maida, A., Hass, D., Escamilla-Ayala, A., Puentes, L.P., Lenberg, J., Friedman, J., Scale, C., Proneth, B., Henkelmann, B., Aldrovandi, M., Agostinis, P., Zimprich, A., Vogt-Weisenhorn, D., Holter-Koch, S., Lewerenz, J., Steinacker, P., Garcia-Saez, A.J., Wurst, W., Tietze, A., Mann, M., Westmeyer, G.G., Friese, M.A., Ramesh, S.K., Wigby, K., Sattler, M., Ingold, I., Ayton, S., Jayavelu, A.K., Popowicz, G., Conrad, M.

To be published.

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: 19.58 kDa 
• Atom Count: 1,420 
• Modeled Residue Count: 165 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipid hydroperoxide glutathione peroxidase	A	172	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.292 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.235	α = 90
b = 45.642	β = 90
c = 84.514	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Bostock, M.J., Mourao, A., Napolitano, V., Sattler, M., Conrad, M., Popowicz, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release