2DYB | pdb_00002dyb

The crystal structure of human p40(phox)

• PDB DOI: https://doi.org/10.2210/pdb2DYB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-09-08 Released: 2007-01-23 
• Deposition Author(s): Honbou, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.302 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Models: experimental

Literature

Full-length p40phox structure suggests a basis for regulation mechanism of its membrane binding.

Honbou, K., Minakami, R., Yuzawa, S., Takeya, R., Suzuki, N.N., Kamakura, S., Sumimoto, H., Inagaki, F.

(2007) EMBO J 26: 1176-1186

• PubMed: 17290225 
• DOI: https://doi.org/10.1038/sj.emboj.7601561
• Primary Citation Related Structures: 
  2DYB


• PubMed Abstract: 
  

  The superoxide-producing phagocyte NADPH oxidase is activated during phagocytosis to destroy ingested microbes. The adaptor protein p40phox associates via the PB1 domain with the essential oxidase activator p67phox, and is considered to function by recruiting p67phox to phagosomes; in this process, the PX domain of p40phox binds to phosphatidylinositol 3-phosphate [PtdIns(3)P], a lipid abundant in the phagosomal membrane. Here we show that the PtdIns(3)P-binding activity of p40phox is normally inhibited by the PB1 domain both in vivo and in vitro. The crystal structure of the full-length p40phox reveals that the inhibition is mediated via intramolecular interaction between the PB1 and PX domains. The interface of the p40phox PB1 domain for the PX domain localizes on the opposite side of that for the p67phox PB1 domain, and thus the PB1-mediated PX regulation occurs without preventing the PB1-PB1 association with p67phox.

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Organizational Affiliation: 
• Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.66 kDa 
• Atom Count: 4,252 
• Modeled Residue Count: 571 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil cytosol factor 4	A, B	341	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15080 (Homo sapiens) Explore Q15080  Go to UniProtKB:  Q15080
PHAROS:  Q15080 GTEx:  ENSG00000100365

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A, B	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.302 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.273	α = 90
b = 189.813	β = 90
c = 79.883	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Honbou, K.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary