6SZ5 | pdb_00006sz5

Human calmodulin bound to a peptide of human NADPH oxidase 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.294 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6SZ5

This is version 1.2 of the entry. See complete history

Literature

On the mechanism of calcium-dependent activation of NADPH oxidase 5 (NOX5).

Millana Fananas, E.Todesca, S.Sicorello, A.Masino, L.Pompach, P.Magnani, F.Pastore, A.Mattevi, A.

(2020) FEBS J 287: 2486-2503

  • DOI: https://doi.org/10.1111/febs.15160
  • Primary Citation Related Structures: 
    6SZ5

  • PubMed Abstract: 

    It is now accepted that reactive oxygen species (ROS) are not only dangerous oxidative agents but also chemical mediators of the redox cell signaling and innate immune response. A central role in ROS-controlled production is played by the NADPH oxidases (NOXs), a group of seven membrane-bound enzymes (NOX1-5 and DUOX1-2) whose unique function is to produce ROS. Here, we describe the regulation of NOX5, a widespread family member present in cyanobacteria, protists, plants, fungi, and the animal kingdom. We show that the calmodulin-like regulatory EF-domain of NOX5 is partially unfolded and detached from the rest of the protein in the absence of calcium. In the presence of calcium, the C-terminal lobe of the EF-domain acquires an ordered and more compact structure that enables its binding to the enzyme dehydrogenase (DH) domain. Our spectroscopic and mutagenesis studies further identified a set of conserved aspartate residues in the DH domain that are essential for NOX5 activation. Altogether, our work shows that calcium induces an unfolded-to-folded transition of the EF-domain that promotes direct interaction with a conserved regulatory region, resulting in NOX5 activation.


  • Organizational Affiliation
    • Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Italy.

Macromolecule Content 

  • Total Structure Weight: 181.25 kDa 
  • Atom Count: 1,362 
  • Modeled Residue Count: 165 
  • Deposited Residue Count: 1,587 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calmodulin-2149Homo sapiensMutation(s): 0 
Gene Names: CALM2CAM2CAMB
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP24 (Homo sapiens)
Explore P0DP24 
Go to UniProtKB:  P0DP24
PHAROS:  P0DP24
GTEx:  ENSG00000143933 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP24
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NADPH oxidase 5
B, C
719Homo sapiensMutation(s): 0 
EC: 1.6.3 (PDB Primary Data), 1 (UniProt)
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.294 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.759α = 90
b = 60.84β = 90
c = 102.444γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG19808

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description