Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 16.97 kDa 
• Atom Count: 1436 
• Modelled Residue Count: 146 
• Deposited Residue Count: 148 
• Unique protein chains: 2

1W70

SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox

• DOI: 10.2210/pdb1W70/pdb

• Classification: SH3 DOMAIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-26 Released: 2005-01-18 
• Deposition Author(s): Massenet, C., Chenavas, S., Cohen-Addad, C., Dagher, M.-C., Brandolin, G., Pebay-Peyroula, E., Fieschi, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.207 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Literature

Effects of P47Phox C-Terminus Phosphorylation on Binding Interactions with P40Phox and P67Phox: Structural and Functional Comparison of P40Phox P67Phox SH3 Domains

Massenet, C., Chenavas, S., Cohen-Addad, C., Dagher, M.-C., Brandolin, G., Pebay-Peyroula, E., Fieschi, F.

(2005) J Biol Chem 280: 13752

• PubMed: 15657040 
• DOI: 10.1074/jbc.M412897200
• Primary Citation of Related Structures:  
  1W70, 1W6X


• PubMed Abstract: 
  

The neutrophil NADPH oxidase produces superoxide anions in response to infection. This reaction is activated by association of cytosolic factors, p47phox and p67phox, and a small G protein Rac with the membranous flavocytochrome b558. Another cytosolic factor, p40phox, is associated to the complex and is reported to play regulatory roles. Initiation of the NADPH oxidase activation cascade has been reported as consecutive to phosphorylation on serines 359/370 and 379 of the p47phox C terminus. These serines surround a polyproline motif that can interact with the Src homology 3 (SH3) module of p40phox (SH3p40) or the C-terminal SH3 of p67phox (C-SH3p67). The latter one presents a higher affinity in the resting state for p47phox. A change in SH3 binding preference following phosphorylation has been postulated earlier. Here we report the crystal structures of SH3p40 alone or in complex with a 12-residue proline-rich region of p47phox at 1.46 angstrom resolution. Using intrinsic tryptophan fluorescence measurements, we compared the affinity of the strict polyproline motif and the whole C terminus peptide with both SH3p40 and C-SH3p67. These data reveal that SH3p40 can interact with a consensus polyproline motif but also with a noncanonical motif of the p47phox C terminus. The electrostatic surfaces of both SH3 are very different, and therefore the binding preference for C-SH3p67 can be attributed to the polyproline motif recognition and particularly to the Arg-368p47 binding mode. The noncanonical motif contributes equally to interaction with both SH3. The influence of serine phosphorylation on residues 359/370 and 379 on the affinity for both SH3 domains has been checked. We conclude that contrarily to previous suggestions, phosphorylation of Ser-359/370 does not modify the SH3 binding affinity for both SH3, whereas phosphorylation of Ser-379 has a destabilizing effect on both interactions. Other mechanisms than a phosphorylation induced switch between the two SH3 must therefore take place for NADPH oxidase activation cascade to start.

---

Organizational Affiliation: 

Institut de Biologie Structurale, UMR 5075 CEA/CNRS/Université Joseph Fourier, Laboratoire des Protéines Membranaires, 41 rue Jules Horowitz 38027 Grenoble cedex 1, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL CYTOSOL FACTOR 4	A, B	60	Homo sapiens	Mutation(s): 0  Gene Names: NCF4, SH3PXD4
Find proteins for Q15080 (Homo sapiens) Explore Q15080  Go to UniProtKB:  Q15080
NIH Common Fund Data Resources
PHAROS:  Q15080 GTEx:  ENSG00000100365

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL CYTOSOL FACTOR 1	C, D	14	Homo sapiens	Mutation(s): 0  Gene Names: NCF1, NOXO2, SH3PXD1A
Find proteins for P14598 (Homo sapiens) Explore P14598  Go to UniProtKB:  P14598
NIH Common Fund Data Resources
PHAROS:  P14598 GTEx:  ENSG00000158517

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	B	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.207 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.64	α = 90
b = 50.49	β = 90
c = 68.18	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-26 
• Released Date: 2005-01-18 
Deposition Author(s): Massenet, C., Chenavas, S., Cohen-Addad, C., Dagher, M.-C., Brandolin, G., Pebay-Peyroula, E., Fieschi, F.

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-05-22
  Changes: Data collection, Experimental preparation