Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Predict Membrane 

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.26 kDa 
• Atom Count: 580 
• Modelled Residue Count: 74 
• Deposited Residue Count: 74 
• Unique protein chains: 1

2M59

Spatial structure of dimeric VEGFR2 membrane domain in DPC micelles

• PDB DOI: 10.2210/pdb2M59/pdb
• BMRB: 19041

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-02-19 Released: 2014-03-12 
• Deposition Author(s): Mineev, K.S., Arseniev, A.S., Shulepko, M.A., Lyukmanova, E.N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

Structural and functional characterization of alternative transmembrane domain conformations in VEGF receptor 2 activation.

Manni, S., Mineev, K.S., Usmanova, D., Lyukmanova, E.N., Shulepko, M.A., Kirpichnikov, M.P., Winter, J., Matkovic, M., Deupi, X., Arseniev, A.S., Ballmer-Hofer, K.

(2014) Structure 22: 1077-1089

• PubMed: 24980797 
• DOI: 10.1016/j.str.2014.05.010
• Primary Citation of Related Structures:  
  2M59, 2MET, 2MEU


• PubMed Abstract: 
  

Transmembrane signaling by receptor tyrosine kinases (RTKs) entails ligand-mediated dimerization and structural rearrangement of the extracellular domains. RTK activation also depends on the specific orientation of the transmembrane domain (TMD) helices, as suggested by pathogenic, constitutively active RTK mutants. Such mutant TMDs carry polar amino acids promoting stable transmembrane helix dimerization, which is essential for kinase activation. We investigated the effect of polar amino acids introduced into the TMD of vascular endothelial growth factor receptor 2, regulating blood vessel homeostasis. Two mutants showed constitutive kinase activity, suggesting that precise TMD orientation is mandatory for kinase activation. Nuclear magnetic resonance spectroscopy revealed that TMD helices in activated constructs were rotated by 180° relative to the interface of the wild-type conformation, confirming that ligand-mediated receptor activation indeed results from transmembrane helix rearrangement. A molecular dynamics simulation confirmed the transmembrane helix arrangement of wild-type and mutant TMDs revealed by nuclear magnetic resonance spectroscopy.

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Organizational Affiliation: 

Paul Scherrer Institute, Biomolecular Research, 5232 Villigen PSI, Switzerland. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A, B	37	Homo sapiens	Mutation(s): 0  Gene Names: KDR, FLK1, VEGFR2 EC: 2.7.10.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens) Explore P35968  Go to UniProtKB:  P35968
PHAROS:  P35968

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 
• OLDERADO: 2M59 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-19 
• Released Date: 2014-03-12 
Deposition Author(s): Mineev, K.S., Arseniev, A.S., Shulepko, M.A., Lyukmanova, E.N.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Database references