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- PDB-2f37: Crystal structure of the ankyrin repeat domain of human TRPV2 -

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Basic information

Entry
Database: PDB / ID: 2f37
TitleCrystal structure of the ankyrin repeat domain of human TRPV2
ComponentsTransient receptor potential cation channel subfamily V member 2
KeywordsMEMBRANE PROTEIN / ankyrin repeat
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / growth cone membrane / sensory perception / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / plasma membrane => GO:0005886 / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone ...monoatomic ion transmembrane transporter activity / growth cone membrane / sensory perception / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / plasma membrane => GO:0005886 / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium ion transmembrane transport / calcium channel activity / melanosome / cell body / monoatomic ion channel activity / positive regulation of cold-induced thermogenesis / response to heat / cell surface / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 2 / Domain of unknown function DUF3447 / Transient receptor potential cation channel subfamily V member 1-4 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...Transient receptor potential cation channel subfamily V member 2 / Domain of unknown function DUF3447 / Transient receptor potential cation channel subfamily V member 1-4 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ion transport domain / Ion transport protein / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMcCleverty, C.J.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of the human TRPV2 channel ankyrin repeat domain.
Authors: McCleverty, C.J. / Koesema, E. / Patapoutian, A. / Lesley, S.A. / Kreusch, A.
History
DepositionNov 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 2
B: Transient receptor potential cation channel subfamily V member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0154
Polymers55,8232
Non-polymers1922
Water7,008389
1
A: Transient receptor potential cation channel subfamily V member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0072
Polymers27,9111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transient receptor potential cation channel subfamily V member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0072
Polymers27,9111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.657, 93.657, 265.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-682-

HOH

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Components

#1: Protein Transient receptor potential cation channel subfamily V member 2 / TrpV2 / osm-9-like TRP channel 2 / OTRPC2 / Vanilloid receptor-like protein 1 / VRL-1


Mass: 27911.254 Da / Num. of mol.: 2 / Fragment: ankyrin repeat domain (residues 69-319)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV2, VRL / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9Y5S1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 1.5 M Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 83694 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.65→1.68 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22862 3848 5 %RANDOM
Rwork0.2066 ---
all0.21 83694 --
obs0.20771 72681 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 10 389 4287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223968
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9745397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2595515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43624.67182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50415677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2451525
X-RAY DIFFRACTIONr_chiral_restr0.3730.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023011
X-RAY DIFFRACTIONr_nbd_refined0.2130.22097
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2365
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.9340.219
X-RAY DIFFRACTIONr_mcbond_it11.52507
X-RAY DIFFRACTIONr_mcangle_it1.67424036
X-RAY DIFFRACTIONr_scbond_it2.05731461
X-RAY DIFFRACTIONr_scangle_it3.2784.51351
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 257 -
Rwork0.262 5266 -
obs--99.84 %

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