Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1BCDE 

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

Macromolecule Content

• Total Structure Weight: 333.84 kDa 
• Atom Count: 23017 
• Residue Count: 2685 
• Unique protein chains: 5

3P8C

Structure and Control of the Actin Regulatory WAVE Complex

• DOI: 10.2210/pdb3P8C/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-13 Released: 2010-12-01 
• Deposition Author(s): Chen, Z., Borek, D., Padrick, S.B., Gomez, T.S., Metlagel, Z., Ismail, A.M., Umetani, J., Billadeau, D.D., Otwinowski, Z., Rosen, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.237 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Structure and control of the actin regulatory WAVE complex.

Chen, Z., Borek, D., Padrick, S.B., Gomez, T.S., Metlagel, Z., Ismail, A.M., Umetani, J., Billadeau, D.D., Otwinowski, Z., Rosen, M.K.

(2010) Nature 468: 533-538

• PubMed: 21107423 
• DOI: 10.1038/nature09623
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Members of the Wiskott-Aldrich syndrome protein (WASP) family control cytoskeletal dynamics by promoting actin filament nucleation with the Arp2/3 complex. The WASP relative WAVE regulates lamellipodia formation within a 400-kilodalton, hetero-pentameric WAVE regulatory complex (WRC). The WRC is inactive towards the Arp2/3 complex, but can be stimulated by the Rac GTPase, kinases and phosphatidylinositols. Here we report the 2.3-ångstrom crystal structure of the WRC and complementary mechanistic analyses. The structure shows that the activity-bearing VCA motif of WAVE is sequestered by a combination of intramolecular and intermolecular contacts within the WRC. Rac and kinases appear to destabilize a WRC element that is necessary for VCA sequestration, suggesting the way in which these signals stimulate WRC activity towards the Arp2/3 complex. The spatial proximity of the Rac binding site and the large basic surface of the WRC suggests how the GTPase and phospholipids could cooperatively recruit the complex to membranes.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nck-associated protein 1	B	1128	Homo sapiens	Mutation(s): 0  Gene Names: NCKAP1, HEM2, KIAA0587, NAP1
Find proteins for Q9Y2A7 (Homo sapiens) Go to UniProtKB:  Q9Y2A7
NIH Common Fund Data Resources
PHAROS  Q9Y2A7 GTEx  ENSG00000061676

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytoplasmic FMR1-interacting protein 1	A	1253	Homo sapiens	Mutation(s): 0  Gene Names: CYFIP1, KIAA0068
Find proteins for Q7L576 (Homo sapiens) Go to UniProtKB:  Q7L576
NIH Common Fund Data Resources
PHAROS  Q7L576 GTEx  ENSG00000273749

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Wiskott-Aldrich syndrome protein family member 1	D	279	Homo sapiens	Mutation(s): 0  Gene Names: WASF1, KIAA0269, SCAR1, WAVE1
Find proteins for Q92558 (Homo sapiens) Go to UniProtKB:  Q92558
NIH Common Fund Data Resources
PHAROS  Q92558 GTEx  ENSG00000112290

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Probable protein BRICK1	E	75	Homo sapiens	Mutation(s): 0  Gene Names: C3orf10, HSPC300, MDS027, BRK1
Find proteins for Q8WUW1 (Homo sapiens) Go to UniProtKB:  Q8WUW1
NIH Common Fund Data Resources
PHAROS  Q8WUW1 GTEx  ENSG00000254999

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Abl interactor 2	F	159	Homo sapiens	Mutation(s): 0  Gene Names: ABI2, ARGBPIA
Find proteins for Q9NYB9 (Homo sapiens) Go to UniProtKB:  Q9NYB9
NIH Common Fund Data Resources
PHAROS  Q9NYB9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.237 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.013	α = 90
b = 113.982	β = 90
c = 327.193	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-13 
• Released Date: 2010-12-01 
Deposition Author(s): Chen, Z., Borek, D., Padrick, S.B., Gomez, T.S., Metlagel, Z., Ismail, A.M., Umetani, J., Billadeau, D.D., Otwinowski, Z., Rosen, M.K.

Revision History 

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2017-08-02
  Changes: Refinement description, Source and taxonomy