5VXA | pdb_00005vxa

Structure of the human Mesh1-NADPH complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.205 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.165 (Depositor) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5VXA

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis.

Ding, C.C.Rose, J.Sun, T.Wu, J.Chen, P.H.Lin, C.C.Yang, W.H.Chen, K.Y.Lee, H.Xu, E.Tian, S.Akinwuntan, J.Zhao, J.Guan, Z.Zhou, P.Chi, J.T.

(2020) Nat Metab 2: 270-277

  • DOI: https://doi.org/10.1038/s42255-020-0181-1
  • Primary Citation Related Structures: 
    5VXA

  • PubMed Abstract: 

    Critical to the bacterial stringent response is the rapid relocation of resources from proliferation toward stress survival through the respective accumulation and degradation of (p)ppGpp by RelA and SpoT homologues. While mammalian genomes encode MESH1, a homologue of the bacterial (p)ppGpp hydrolase SpoT, neither (p)ppGpp nor its synthetase has been identified in mammalian cells. Here, we show that human MESH1 is an efficient cytosolic NADPH phosphatase that facilitates ferroptosis. Visualization of the MESH1-NADPH crystal structure revealed a bona fide affinity for the NADPH substrate. Ferroptosis-inducing erastin or cystine deprivation elevates MESH1, whose overexpression depletes NADPH and sensitizes cells to ferroptosis, whereas MESH1 depletion promotes ferroptosis survival by sustaining the levels of NADPH and GSH and by reducing lipid peroxidation. The ferroptotic protection by MESH1 depletion is ablated by suppression of the cytosolic NAD(H) kinase, NADK, but not its mitochondrial counterpart NADK2. Collectively, these data shed light on the importance of cytosolic NADPH levels and their regulation under ferroptosis-inducing conditions in mammalian cells.


  • Organizational Affiliation
    • Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 43.14 kDa 
  • Atom Count: 3,272 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 360 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
A, B
180Homo sapiensMutation(s): 0 
Gene Names: HDDC3MESH1
EC: 3.1.7.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4P3 (Homo sapiens)
Explore Q8N4P3 
Go to UniProtKB:  Q8N4P3
PHAROS:  Q8N4P3
GTEx:  ENSG00000184508 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N4P3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
M [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
BME

Query on BME



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.205 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.165 (Depositor) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.78α = 90
b = 80.37β = 90
c = 114.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-30
    Changes: Database references, Derived calculations