2F37 | pdb_00002f37

Crystal structure of the ankyrin repeat domain of human TRPV2

• PDB DOI: https://doi.org/10.2210/pdb2F37/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-18 Released: 2006-10-31 
• Deposition Author(s): McCleverty, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of the human TRPV2 channel ankyrin repeat domain.

McCleverty, C.J., Koesema, E., Patapoutian, A., Lesley, S.A., Kreusch, A.

(2006) Protein Sci 15: 2201-2206

• PubMed: 16882997 
• DOI: https://doi.org/10.1110/ps.062357206
• Primary Citation Related Structures: 
  2F37


• PubMed Abstract: 
  

  TRPV channels are important polymodal integrators of noxious stimuli mediating thermosensation and nociception. An ankyrin repeat domain (ARD), which is a common protein-protein recognition domain, is conserved in the N-terminal intracellular domain of all TRPV channels and predicted to contain three to four ankyrin repeats. Here we report the first structure from the TRPV channel subfamily, a 1.7 A resolution crystal structure of the human TRPV2 ARD. Our crystal structure reveals a six ankyrin repeat stack with multiple insertions in each repeat generating several unique features compared with a canonical ARD. The surface typically used for ligand recognition, the ankyrin groove, contains extended loops with an exposed hydrophobic patch and a prominent kink resulting from a large rotational shift of the last two repeats. The TRPV2 ARD provides the first structural insight into a domain that coordinates nociceptive sensory transduction and is likely to be a prototype for other TRPV channel ARDs.

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Organizational Affiliation: 
• Genomics Institute of the Novartis Research Foundation, CA 92121, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.01 kDa 
• Atom Count: 4,287 
• Modeled Residue Count: 496 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 2	A, B	251	Homo sapiens	Mutation(s): 3  Gene Names: TRPV2, VRL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5S1 (Homo sapiens) Explore Q9Y5S1  Go to UniProtKB:  Q9Y5S1
PHAROS:  Q9Y5S1 GTEx:  ENSG00000187688

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.657	α = 90
b = 93.657	β = 90
c = 265.855	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): McCleverty, C.J.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary