5O0T | pdb_00005o0t

CRYSTAL STRUCTURE OF TRANS-MEMBRANE DOMAIN OF Cylindrospermum stagnale NADPH-OXIDASE 5 (NOX5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5O0T

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structures and atomic model of NADPH oxidase.

Magnani, F.Nenci, S.Millana Fananas, E.Ceccon, M.Romero, E.Fraaije, M.W.Mattevi, A.

(2017) Proc Natl Acad Sci U S A 114: 6764-6769

  • DOI: https://doi.org/10.1073/pnas.1702293114
  • Primary Citation Related Structures: 
    5O0T, 5O0X

  • PubMed Abstract: 

    NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.


  • Organizational Affiliation
    • Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, 27100 Pavia, Italy; francesca.magnani@unipv.it andrea.mattevi@unipv.it.

Macromolecule Content 

  • Total Structure Weight: 26.59 kDa 
  • Atom Count: 1,918 
  • Modeled Residue Count: 206 
  • Deposited Residue Count: 206 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ferric reductase206Cylindrospermum stagnale PCC 7417Mutation(s): 5 
Gene Names: Cylst_1289
Membrane Entity: Yes 
UniProt
Find proteins for K9WT99 (Cylindrospermum stagnale PCC 7417)
Explore K9WT99 
Go to UniProtKB:  K9WT99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9WT99
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LFA

Query on LFA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
D10

Query on D10



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.371α = 90
b = 74.57β = 90
c = 85.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry for Science and EducationItalyPRIN2015-20152TE5PK_004

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references