8U87 | pdb_00008u87

Structural Basis of Human NOX5 Activation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of human NOX5 activation.

Cui, C.Jiang, M.Jain, N.Das, S.Lo, Y.H.Kermani, A.A.Pipatpolkai, T.Sun, J.

(2024) Nat Commun 15: 3994-3994

  • DOI: https://doi.org/10.1038/s41467-024-48467-y
  • Primary Citation of Related Structures:  
    8U7Y, 8U85, 8U86, 8U87

  • PubMed Abstract: 

    NADPH oxidase 5 (NOX5) catalyzes the production of superoxide free radicals and regulates physiological processes from sperm motility to cardiac rhythm. Overexpression of NOX5 leads to cancers, diabetes, and cardiovascular diseases. NOX5 is activated by intracellular calcium signaling, but the underlying molecular mechanism of which - in particular, how calcium triggers electron transfer from NADPH to FAD - is still unclear. Here we capture motions of full-length human NOX5 upon calcium binding using single-particle cryogenic electron microscopy (cryo-EM). By combining biochemistry, mutagenesis analyses, and molecular dynamics (MD) simulations, we decode the molecular basis of NOX5 activation and electron transfer. We find that calcium binding to the EF-hand domain increases NADPH dynamics, permitting electron transfer between NADPH and FAD and superoxide production. Our structural findings also uncover a zinc-binding motif that is important for NOX5 stability and enzymatic activity, revealing modulation mechanisms of reactive oxygen species (ROS) production.


  • Organizational Affiliation
    • Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADPH oxidase 5A,
B [auth C]
719Homo sapiensMutation(s): 0 
Gene Names: NOX5
EC: 1.6.3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PH1 (Homo sapiens)
Explore Q96PH1 
Go to UniProtKB:  Q96PH1
PHAROS:  Q96PH1
GTEx:  ENSG00000255346 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PH1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEB (Subject of Investigation/LOI)
Query on HEB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth C],
I [auth C]
HEME B/C
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-RGGAHWMASA-L
D12
Query on D12

Download Ideal Coordinates CCD File 
L [auth C]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM141357

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary