Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 75.35 kDa 
• Atom Count: 5584 
• Residue Count: 638 
• Unique protein chains: 3

2A3Z

Ternary complex of the WH2 domain of WASP with Actin-DNAse I

• DOI: 10.2210/pdb2A3Z/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Oryctolagus cuniculus, Bos taurus
• Mutation(s): Yes 


• Deposited: 2005-06-27 Released: 2005-11-01 
• Deposition Author(s): Chereau, D., Kerff, F., Dominguez, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.210 
• R-Value Work: 0.153 
• R-Value Observed: 0.159 

Literature

Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly

Chereau, D., Kerff, F., Graceffa, P., Grabarek, Z., Langsetmo, K., Dominguez, R.

(2005) Proc Natl Acad Sci U S A 102: 16644-16649

• PubMed: 16275905 
• DOI: 10.1073/pnas.0507021102
• Primary Citation of Related Structures:  
  2A40, 2A3Z, 2A42, 2A41


• PubMed Abstract: 
  

Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) is a small and widespread actin-binding motif. In the WASP family, WH2 plays a role in filament nucleation by Arp2/3 complex. Here we describe the crystal structures of complexes of actin with the WH2 domains of WASP, WASP-family verprolin homologous protein, and WASP-interacting protein. Despite low sequence identity, WH2 shares structural similarity with the N-terminal portion of the actin monomer-sequestering thymosin beta domain (Tbeta). We show that both domains inhibit nucleotide exchange by targeting the cleft between actin subdomains 1 and 3, a common binding site for many unrelated actin-binding proteins. Importantly, WH2 is significantly shorter than Tbeta but binds actin with approximately 10-fold higher affinity. WH2 lacks a C-terminal extension that in Tbeta4 becomes involved in monomer sequestration by interfering with intersubunit contacts in F-actin. Owing to their shorter length, WH2 domains connected in tandem by short linkers can coexist with intersubunit contacts in F-actin and are proposed to function in filament nucleation by lining up actin subunits along a filament strand. The WH2-central region of WASP-family proteins is proposed to function in an analogous way by forming a special class of tandem repeats whose function is to line up actin and Arp2 during Arp2/3 nucleation. The structures also suggest a mechanism for how profilin-binding Pro-rich sequences positioned N-terminal to WH2 could feed actin monomers directly to WH2, thereby playing a role in filament elongation.

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Organizational Affiliation: 

Boston Biomedical Research Institute, Watertown, MA 02472, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	375	Oryctolagus cuniculus	Mutation(s): 1  Gene Names: ACTA1, ACTA
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribonuclease-1	B	260	Bos taurus	Mutation(s): 0  Gene Names: DNASE1, DNL1 EC: 3.1.21.1
Find proteins for P00639 (Bos taurus) Explore P00639  Go to UniProtKB:  P00639

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Wiskott-Aldrich syndrome protein	C	29	N/A	Mutation(s): 0
Find proteins for P42768 (Homo sapiens) Explore P42768  Go to UniProtKB:  P42768
NIH Common Fund Data Resources
PHAROS  P42768 GTEx  ENSG00000015285

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	A	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	B	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.210 
• R-Value Work: 0.153 
• R-Value Observed: 0.159 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.27	α = 90
b = 41.798	β = 108.68
c = 119.418	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-27 
• Released Date: 2005-11-01 
Deposition Author(s): Chereau, D., Kerff, F., Dominguez, R.

Revision History 

• Version 1.0: 2005-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary