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

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Basic information

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


growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation transmembrane transport / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation transmembrane transport / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity / melanosome / lamellipodium / cell body / positive regulation of cold-induced thermogenesis / axon / negative regulation of cell population proliferation / cell surface / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJin, X. / Gaudet, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the N-terminal Ankyrin Repeat Domain of the TRPV2 Ion Channel.
Authors: Jin, X. / Touhey, J. / Gaudet, R.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE The SWS database reference Q9WUD2 conflicts with the citation, Caterina et al, 1999, ...SEQUENCE The SWS database reference Q9WUD2 conflicts with the citation, Caterina et al, 1999, Nature involving residue 151. Sequence in this entry agrees with the citation.

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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


Theoretical massNumber of molelcules
Total (without water)57,0672
Polymers57,0672
Non-polymers00
Water4,990277
1
A: Transient receptor potential cation channel subfamily V member 2


Theoretical massNumber of molelcules
Total (without water)28,5341
Polymers28,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transient receptor potential cation channel subfamily V member 2


Theoretical massNumber of molelcules
Total (without water)28,5341
Polymers28,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.770, 60.770, 339.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer in the asymmetric unit.

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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 / Stretch- ...TrpV2 / osm-9-like TRP channel 2 / OTRPC2 / Vanilloid receptor-like protein 1 / VRL-1 / Stretch-activated channel 2B


Mass: 28533.598 Da / Num. of mol.: 2 / Fragment: residues 75-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv2, Sac2b, Vrl1 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WUD2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17mM protein, 1.2M lithium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→38 Å / Num. all: 33854 / Num. obs: 33406 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.101 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.838 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.202
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24161 3359 10.1 %RANDOM
Rwork0.18937 ---
all0.26 31792 --
obs0.19465 30005 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 0 277 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223823
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9725182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74924.713174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51915665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7691520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022874
X-RAY DIFFRACTIONr_nbd_refined0.210.21787
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.26
X-RAY DIFFRACTIONr_mcbond_it0.7491.52455
X-RAY DIFFRACTIONr_mcangle_it1.31923834
X-RAY DIFFRACTIONr_scbond_it2.13131541
X-RAY DIFFRACTIONr_scangle_it3.3024.51348
LS refinement shellResolution: 2.199→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 250 -
Rwork0.212 2101 -
obs--97.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
118.6246-0.6453-2.814518.4123-11.002420.3378-0.33220.7149-1.9316-0.9070.92511.15920.358-0.8995-0.59280.0090.0026-0.00740.0229-0.01430.008912.74834.93840.83
23.78240.5444-1.91721.204-0.21042.39980.2051-0.6115-0.36040.3323-0.38570.0996-0.06330.2990.18050.1051-0.1140.02680.04290.02740.00630.57638.77774.209
33.59751.4441-1.6176.5328-0.84443.03990.4746-0.08460.33810.4007-0.2588-0.0125-0.59270.1762-0.21580.2061-0.09610.0908-0.0797-0.0338-0.06721.18749.90870.399
41.81230.07547.26440.00310.302329.1188-0.09260.9750.0923-0.7252-0.28380.0825-0.47070.39670.37640.0170.00410.01640.02250.02340.0085-13.93321.00642.61
52.85640.53071.97651.14190.31254.2060.0385-0.234-0.02430.1012-0.0173-0.040.07220.193-0.02120.0009-0.03140.00540.0507-0.0183-0.0931-5.85120.42966.374
62.644-1.58071.72122.7317-1.68113.43720.12790.195-0.0329-0.1222-0.18540.15850.169-0.17030.05750.0489-0.0383-0.0047-0.009-0.038-0.053-8.57322.59266.613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA75 - 891 - 15
2X-RAY DIFFRACTION2AA90 - 23816 - 164
3X-RAY DIFFRACTION3AA239 - 319165 - 245
4X-RAY DIFFRACTION4BB75 - 851 - 11
5X-RAY DIFFRACTION5BB86 - 19812 - 124
6X-RAY DIFFRACTION6BB199 - 320125 - 246

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