Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.76 kDa 
• Atom Count: 1030 
• Modelled Residue Count: 122 
• Deposited Residue Count: 131 
• Unique protein chains: 2

2LNW

Identification and structural basis for a novel interaction between Vav2 and Arap3

• DOI: 10.2210/pdb2LNW/pdb
• BMRB: 18182

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-05 Released: 2012-11-21 
• Deposition Author(s): Wu, B., Zhang, J., Wu, J., Shi, Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Identification and structural basis for a novel interaction between Vav2 and Arap3.

Wu, B., Wang, F., Zhang, J., Zhang, Z., Qin, L., Peng, J., Li, F., Liu, J., Lu, G., Gong, Q., Yao, X., Wu, J., Shi, Y.

(2012) J Struct Biol 180: 84-95

• PubMed: 22750419 
• DOI: 10.1016/j.jsb.2012.06.011
• Primary Citation of Related Structures:  
  2LNX, 2LNW


• PubMed Abstract: 
  

Vav2 is a ubiquitous guanine nucleotide exchange factor (GEF) for the small GTPase Rac1. It regulates processes including cell migration, neuronal development and phagocytosis through interactions with different proteins. In this study, Arap3, a dual GTPase-activating protein (GAP) for RhoA and Arf6, was first identified to be a novel interaction partner for Vav2 both in vitro and in vivo. ITC and NMR chemical shift perturbation experiments demonstrated that Vav2 SH2 domain was able to interact directly with phosphorylated Y1403 and Y1408 within the C-terminal region of Arap3 with high affinities, with the dissociation constants (Kd) of ≈ 0.27 and ≈ 1.40 μM, respectively. In addition, using different phosphotyrosine peptides, the pY +3 specificity of Vav2 SH2 domain was discovered. The solution structures of Vav2 SH2 domain in free and in complex with the phosphotyrosine peptide pY1408 were therefore determined to understand the structural basis of this recognition specificity. Structural analysis revealed that the presence of a Phe residue in the BG loop (BG6) leads to the formation of a shallow hydrophobic pY +3 pocket on the surface of Vav2 SH2 domain, which determines the pY +3 specificity of Vav2 SH2 domain.

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide exchange factor VAV2	A	122	Homo sapiens	Mutation(s): 0  Gene Names: VAV2
Find proteins for P52735 (Homo sapiens) Explore P52735  Go to UniProtKB:  P52735
NIH Common Fund Data Resources
PHAROS:  P52735 GTEx:  ENSG00000160293

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3	B	9	Homo sapiens	Mutation(s): 0  Gene Names: ARAP3, CENTD3
Find proteins for Q8WWN8 (Homo sapiens) Explore Q8WWN8  Go to UniProtKB:  Q8WWN8
NIH Common Fund Data Resources
PHAROS:  Q8WWN8 GTEx:  ENSG00000120318

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LNW Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-05 
• Released Date: 2012-11-21 
Deposition Author(s): Wu, B., Zhang, J., Wu, J., Shi, Y.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release