2A40

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

• PDB DOI: https://doi.org/10.2210/pdb2A40/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Oryctolagus cuniculus, Bos taurus, Homo sapiens
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 151.84 kDa 
• Atom Count: 11,357 
• Modelled Residue Count: 1,288 
• Deposited Residue Count: 1,334 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, D	375	Oryctolagus cuniculus	Mutation(s): 0
UniProt
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, E	260	Bos taurus	Mutation(s): 0  EC: 3.1.21.1
UniProt
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 family member 2	C, F	32	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6W5 (Homo sapiens) Explore Q9Y6W5  Go to UniProtKB:  Q9Y6W5
PHAROS:  Q9Y6W5 GTEx:  ENSG00000158195

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	J [auth A], P [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL	K [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], L [auth B], O [auth D], Q [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	M [auth B], R [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.719	α = 90
b = 41.598	β = 108.79
c = 153.048	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary