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- PDB-3jxi: Crystal structure of the chicken TRPV4 ankyrin repeat domain -

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Basic information

Entry
Database: PDB / ID: 3jxi
TitleCrystal structure of the chicken TRPV4 ankyrin repeat domain
ComponentsVanilloid receptor-related osmotically activated channel protein
KeywordsMEMBRANE PROTEIN / ankyrin repeats / ANK repeat / Ion transport / Ionic channel / Receptor / Transmembrane / Transport
Function / homology
Function and homology information


osmosensory signaling pathway / monoatomic cation channel activity / adherens junction / calcium channel activity / intracellular calcium ion homeostasis / calmodulin binding / apical plasma membrane / lipid binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 4 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential cation channel subfamily V member 4 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / 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 4 / Transient receptor potential cation channel subfamily V member 4
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPhelps, C.B. / Wang, R.R. / Gaudet, R.
CitationJournal: Nat.Genet. / Year: 2010
Title: Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.
Authors: Landoure, G. / Zdebik, A.A. / Martinez, T.L. / Burnett, B.G. / Stanescu, H.C. / Inada, H. / Shi, Y. / Taye, A.A. / Kong, L. / Munns, C.H. / Choo, S.S. / Phelps, C.B. / Paudel, R. / Houlden, ...Authors: Landoure, G. / Zdebik, A.A. / Martinez, T.L. / Burnett, B.G. / Stanescu, H.C. / Inada, H. / Shi, Y. / Taye, A.A. / Kong, L. / Munns, C.H. / Choo, S.S. / Phelps, C.B. / Paudel, R. / Houlden, H. / Ludlow, C.L. / Caterina, M.J. / Gaudet, R. / Kleta, R. / Fischbeck, K.H. / Sumner, C.J.
History
DepositionSep 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vanilloid receptor-related osmotically activated channel protein
B: Vanilloid receptor-related osmotically activated channel protein
C: Vanilloid receptor-related osmotically activated channel protein
D: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)117,9164
Polymers117,9164
Non-polymers00
Water9,620534
1
A: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)29,4791
Polymers29,4791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)29,4791
Polymers29,4791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)29,4791
Polymers29,4791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)29,4791
Polymers29,4791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.259, 48.119, 133.891
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Vanilloid receptor-related osmotically activated channel protein


Mass: 29478.891 Da / Num. of mol.: 4 / Fragment: UNP residues 133-382, ankyrin repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TRPV4, VR-OAC / Plasmid: pET21-C6H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9DFS3, UniProt: A0A1D5PXA5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium citrate pH 5.0, 10% MPD, 2% PEG8000, 4.3% trifluoroethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2007 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 65393 / % possible obs: 97.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.078 / Χ2: 1.507 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.282.70.59864571.633197.1
2.28-2.372.80.41764401.213197.6
2.37-2.482.80.3364551.321197.3
2.48-2.612.80.26764861.388197.3
2.61-2.772.80.21764691.586197.1
2.77-2.992.80.13965251.609197.4
2.99-3.292.80.10565141.776197.7
3.29-3.762.90.07566011.931198.2
3.76-4.742.90.04866741.551198.6
4.74-352.90.03467721.067197.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2etb (TRPV2 ankyrin repeats)

2etb


Resolution: 2.3→29.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.892 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.221 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1178 2 %RANDOM
Rwork0.203 ---
obs0.204 57722 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.79 Å2 / Biso mean: 27.512 Å2 / Biso min: 3.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.02 Å2
2--0.23 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8005 0 0 534 8539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228184
X-RAY DIFFRACTIONr_bond_other_d0.0010.025703
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.96611049
X-RAY DIFFRACTIONr_angle_other_deg1.007313845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74451009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76723.111389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.951151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671573
X-RAY DIFFRACTIONr_chiral_restr0.0850.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021705
X-RAY DIFFRACTIONr_mcbond_it0.5631.55019
X-RAY DIFFRACTIONr_mcbond_other0.1331.52036
X-RAY DIFFRACTIONr_mcangle_it1.04928073
X-RAY DIFFRACTIONr_scbond_it1.74533165
X-RAY DIFFRACTIONr_scangle_it2.7924.52972
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 79 -
Rwork0.249 4089 -
all-4168 -
obs--97.66 %
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)
15.5523-0.3693-4.81082.95010.71476.1402-0.0307-0.5343-0.16050.2561-0.1746-0.25550.11990.24340.20530.0761-0.0019-0.08860.16030.00790.3049-29.3551-13.996210.3746
23.07080.5182-0.98392.5197-1.42673.08430.0027-0.0217-0.08530.0378-0.0653-0.00990.0473-0.03050.06250.05390.0106-0.05420.0886-0.00550.2225-35.7376-10.67212.6802
33.2828-0.12310.23672.4853-1.26662.77210.06040.1360.0837-0.0903-0.0896-0.1450.01140.18290.02910.05230.0196-0.03010.1127-0.02610.2035-41.5085-3.2286-6.1198
43.1606-0.92890.47222.3027-0.92382.86850.15790.4374-0.0602-0.4254-0.1554-0.14890.15620.0907-0.00260.09610.0513-0.04360.1592-0.03370.1826-48.7688-1.3657-17.1689
52.8272-0.2735-0.23835.61911.3653.91470.14820.5582-0.2524-0.2251-0.13870.16050.3334-0.1875-0.00960.14540.0783-0.11520.2938-0.01760.1395-57.05052.0703-23.6111
612.877110.84639.34819.17457.86336.78910.0195-0.4913-0.6072-0.01280.19261.3890.2837-0.4199-0.21210.48040.17550.02190.44120.04020.47-62.8170.9677-34.2671
73.91060.8017-4.17162.7097-1.57045.8251-0.01060.4106-0.0125-0.1447-0.0620.24370.16-0.28870.07260.0559-0.0068-0.07860.14190.00460.2625-24.0229.0799-10.5763
81.963-3.0602-2.97158.91749.11469.46570.09650.16870.2454-0.44440.0921-0.2234-0.44070.1229-0.18860.1157-0.0156-0.04010.10060.03580.228-18.322420.1546-9.7931
93.3610.1893-1.21072.29021.80574.2121-0.1051-0.1131-0.14110.1778-0.04820.13120.1906-0.12030.15320.0887-0.0175-0.05750.07340.02820.2204-16.48349.25-1.6064
103.1147-0.77171.06028.19222.17325.07120.0573-0.09250.205-0.1386-0.08590.2336-0.291-0.37320.02860.0541-0.0071-0.06220.16830.0080.3071-12.941621.43383.4107
113.58270.85430.09221.36350.96782.4531-0.0225-0.094-0.03450.0421-0.00190.13230.1718-0.10440.02440.0657-0.0034-0.06850.12510.02640.1899-8.694217.63656.1611
122.20321.17010.97721.97550.83752.11320.1356-0.3592-0.0450.2525-0.08570.09730.2071-0.1582-0.04990.0834-0.0076-0.03360.13580.02410.1461-0.66422.751119.9028
138.73640.89695.4514.0802-0.61724.98710.3687-0.1195-0.68060.2714-0.1443-0.62670.67440.4536-0.22440.3397-0.0367-0.11420.27880.0410.240512.48620.420834.1708
145.04560.2411-0.58260.89460.10773.6871-0.01590.41430.2494-0.07310.0790.2208-0.2461-0.3489-0.06310.30710.0833-0.13910.37730.07440.1285-47.523924.5657-59.0692
153.53410.43830.79613.18-0.35243.4503-0.13470.2491-0.1608-0.24640.0911-0.12060.06150.15380.04350.28810.0588-0.11640.30780.02810.069-34.231217.6152-50.1398
163.9722-1.47031.41771.8855-0.80522.4602-0.13290.00190.18140.02530.0367-0.1176-0.28640.02770.09620.29660.0233-0.11210.30780.04980.1516-20.442616.7254-38.3691
172.4654-0.3995-1.55084.86552.433115.6154-0.1419-0.14630.28060.2202-0.11850.43970.0474-0.60220.26040.27320.0246-0.02490.28390.01910.3505-6.623218.9707-23.6512
1811.12043.8363-4.93931.3234-1.7042.19391.99240.26450.22631.4259-0.7789-1.38840.98241.5341-1.21350.57020.3984-0.52610.85470.08261.3237-1.381335.7214-65.7347
192.27850.3803-3.065.718-0.15884.13160.86430.7561-0.4753-1.2846-0.03220.9949-0.4956-0.2772-0.83210.61190.2028-0.46640.90610.04071.1229.4435.1046-64.1616
200.7553-1.6587-2.1153.96135.37677.6035-0.04990.9527-0.7750.23040.40040.96450.5468-0.789-0.35060.29030.1975-0.54410.73850.25781.69222.404529.8195-59.0233
214.0601-1.6376-2.97579.2469-0.37325.30370.20470.0184-0.8819-0.1306-0.13841.0507-0.0128-0.0681-0.06640.32480.0479-0.31750.64940.13520.880712.166629.6848-53.0975
225.11190.36191.38058.2052-3.70574.48460.0783-0.0208-0.8367-0.56350.38331.5060.004-0.2501-0.46160.17810.1619-0.25160.46410.1830.860219.930726.3123-47.7821
232.543-2.45280.81573.9736-1.87594.2346-0.0401-0.4641-0.240.39750.3451.2995-0.3066-0.3705-0.30490.16060.1824-0.03550.41790.12250.60430.820220.984-37.6292
242.0051-0.17993.13732.09961.337.7122-0.1807-0.16880.24960.45430.0810.3116-0.1955-0.01520.09970.31110.1297-0.00790.37210.04130.244645.24318.9499-28.9143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A132 - 165
2X-RAY DIFFRACTION2A166 - 210
3X-RAY DIFFRACTION3A211 - 261
4X-RAY DIFFRACTION4A262 - 326
5X-RAY DIFFRACTION5A327 - 374
6X-RAY DIFFRACTION6A375 - 384
7X-RAY DIFFRACTION7B132 - 162
8X-RAY DIFFRACTION8B163 - 178
9X-RAY DIFFRACTION9B179 - 209
10X-RAY DIFFRACTION10B210 - 234
11X-RAY DIFFRACTION11B235 - 259
12X-RAY DIFFRACTION12B264 - 376
13X-RAY DIFFRACTION13B377 - 387
14X-RAY DIFFRACTION14C132 - 210
15X-RAY DIFFRACTION15C211 - 269
16X-RAY DIFFRACTION16C270 - 376
17X-RAY DIFFRACTION17C377 - 388
18X-RAY DIFFRACTION18D132 - 136
19X-RAY DIFFRACTION19D137 - 149
20X-RAY DIFFRACTION20D150 - 181
21X-RAY DIFFRACTION21D182 - 223
22X-RAY DIFFRACTION22D224 - 268
23X-RAY DIFFRACTION23D269 - 367
24X-RAY DIFFRACTION24D368 - 388

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