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- PDB-3w9g: Crystal structure of the ankyrin repeat domain of chicken TRPV4 -

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Basic information

Entry
Database: PDB / ID: 3w9g
TitleCrystal structure of the ankyrin repeat domain of chicken TRPV4
ComponentsVanilloid receptor-related osmotically activated channel protein
KeywordsTRANSPORT PROTEIN / ankyrin repeat domain / ARD
Function / homology
Function and homology information


osmosensory signaling pathway / calcium ion import across plasma membrane / monoatomic cation channel activity / phosphatidylinositol binding / actin filament organization / adherens junction / SH3 domain binding / calcium channel activity / intracellular calcium ion homeostasis / calmodulin binding ...osmosensory signaling pathway / calcium ion import across plasma membrane / monoatomic cation channel activity / phosphatidylinositol binding / actin filament organization / adherens junction / SH3 domain binding / calcium channel activity / intracellular calcium ion homeostasis / calmodulin binding / cilium / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsItoh, Y. / Hamada-nakahara, S. / Suetsugu, S.
CitationJournal: Nat Commun / Year: 2014
Title: TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P2
Authors: Takahashi, N. / Hamada-Nakahara, S. / Itoh, Y. / Takemura, K. / Shimada, A. / Ueda, Y. / Kitamata, M. / Matsuoka, R. / Hanawa-Suetsugu, K. / Senju, Y. / Mori, M.X. / Kiyonaka, S. / Kohda, D. ...Authors: Takahashi, N. / Hamada-Nakahara, S. / Itoh, Y. / Takemura, K. / Shimada, A. / Ueda, Y. / Kitamata, M. / Matsuoka, R. / Hanawa-Suetsugu, K. / Senju, Y. / Mori, M.X. / Kiyonaka, S. / Kohda, D. / Kitao, A. / Mori, Y. / Suetsugu, S.
History
DepositionApr 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 21, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water10,953608
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
5
A: Vanilloid receptor-related osmotically activated channel protein

C: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)58,9582
Polymers58,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area1170 Å2
ΔGint-14 kcal/mol
Surface area24170 Å2
MethodPISA
6
B: Vanilloid receptor-related osmotically activated channel protein

D: Vanilloid receptor-related osmotically activated channel protein


Theoretical massNumber of molelcules
Total (without water)58,9582
Polymers58,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1210 Å2
ΔGint-14 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.952, 48.267, 134.029
Angle α, β, γ (deg.)90.000, 101.790, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TRPV4, VR-OAC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9DFS3, UniProt: A0A1D5PXA5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 110-120mM sodium MES-HCl buffer pH 6.5, 1-2% PEG4000, 11-12% MPD, 55-60mM KH2PO4, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2012 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 89777 / Num. obs: 89687 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 26.51 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8903 / Rsym value: 0.644 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JXI

3jxi


Resolution: 2→37.569 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8516 / SU ML: 0.18 / σ(F): 0 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1819 2.03 %Random
Rwork0.1791 ---
obs0.1798 89579 99.76 %-
all-89795 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.32 Å2 / Biso mean: 48.4734 Å2 / Biso min: 9.6 Å2
Refinement stepCycle: LAST / Resolution: 2→37.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 0 608 8677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088315
X-RAY DIFFRACTIONf_angle_d1.11911218
X-RAY DIFFRACTIONf_chiral_restr0.0761245
X-RAY DIFFRACTIONf_plane_restr0.0051460
X-RAY DIFFRACTIONf_dihedral_angle_d13.4013149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0530.26621350.24596573670899
2.053-2.11350.27581500.220667036853100
2.1135-2.18170.20281410.206467096850100
2.1817-2.25960.26741320.196267196851100
2.2596-2.35010.23521210.188367076828100
2.3501-2.4570.22861380.17767446882100
2.457-2.58650.20261300.176167256855100
2.5865-2.74850.21391350.17867626897100
2.7485-2.96070.22121410.175467716912100
2.9607-3.25850.22181410.179567406881100
3.2585-3.72960.18661300.169268326962100
3.7296-4.69750.16981680.148467936961100
4.6975-37.57560.23031570.18936982713999
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)
15.04330.3036-4.44551.4-1.79255.48760.00770.33870.0205-0.04140.01220.17890.212-0.36650.02050.138-0.0241-0.05010.1363-0.03150.2823-24.13028.7836-10.1441
21.4643-0.8011-0.27162.17552.03712.41420.17140.14440.2174-0.2738-0.09690.021-0.3651-0.11150.00110.18090.0095-0.00290.13870.02820.2636-18.649318.9974-7.5774
32.5485-0.4348-1.69041.30261.64533.87990.0194-0.0813-0.1430.1669-0.08490.00870.3547-0.11350.09280.1931-0.0141-0.00790.11490.00960.2352-17.35996.93210.0518
40.9848-0.47690.16163.70573.25263.62170.0703-0.11290.3468-0.11210.021-0.2198-0.2397-0.1184-0.13070.1677-0.00560.01250.11730.01790.2867-12.15822.1176-0.8102
53.45121.29710.58832.11780.32093.70950.1708-0.3671-0.10710.2045-0.11180.12770.2842-0.1237-0.02510.1375-0.0328-0.01540.15540.03670.2444-9.251313.41826.9211
63.94881.03321.09250.2047-0.12754.6674-0.0329-0.62141.04190.289-0.24550.5787-0.7343-0.52370.15550.2794-0.01980.01230.2741-0.11520.54-10.432529.823912.9377
72.12731.1651.01872.70221.30522.0860.2491-0.3338-0.36720.2635-0.1076-0.06270.2745-0.1474-0.09790.1775-0.0407-0.02070.20220.04860.2643-0.557419.565314.6111
85.4855-0.3732-0.79593.49521.78263.21790.7132-1.3145-0.63420.4427-0.38240.10171.1741-0.20670.0430.3944-0.236-0.02370.51440.13420.2479-0.860917.259525.6808
92.12181.64660.82193.17411.05823.59660.0655-0.5096-0.02970.2893-0.0751-0.2630.083-0.066-0.09380.182-0.040.0220.2663-0.00950.22895.58429.792221.3384
107.3907-2.73195.07456.6411-2.58585.84410.3895-0.1936-0.2513-0.0235-0.0745-0.14440.9997-0.5978-0.24670.5562-0.1628-0.01710.41610.00570.2146.668823.043433.195
115.0542-0.1414-3.97752.5851.95144.87690.0172-0.4985-0.28190.1624-0.0235-0.36340.23810.34510.02790.1333-0.0006-0.0480.16850.05120.2933-28.1279-15.079.3253
123.3850.9776-1.18972.195-1.28552.7830.0712-0.1045-0.06260.0665-0.1151-0.0777-0.04210.02530.06420.1124-0.0024-0.01470.10860.00460.2122-34.3264-10.25263.0624
131.2680.34060.80914.8214-3.7183.890.040.03550.17180.2806-0.01630.1286-0.2992-0.0344-0.05110.1479-0.00410.00640.1036-0.04120.2168-40.1534-1.83350.0234
144.1324-1.13810.67291.7078-0.89814.04540.08020.38760.4021-0.1396-0.212-0.2961-0.18460.07620.11020.13450.01410.02930.1371-0.00880.2416-42.9372-2.2891-10.4851
153.1798-1.22690.67144.3772-0.86842.34970.18720.2391-0.5754-0.1902-0.01690.23480.3526-0.0899-0.16130.1669-0.0005-0.03480.1632-0.05420.2456-53.7403-6.4524-12.0368
163.0357-0.87070.39273.6395-0.56913.04470.19970.7243-0.2429-0.6048-0.1440.0470.31560.0975-0.06550.27610.0689-0.0110.3478-0.04730.1616-54.38711.258-23.5526
176.4793-1.11742.09172.0992-0.46136.6050.46690.2745-0.3855-0.64970.24280.91610.6403-0.4459-0.64690.59210.1059-0.1380.60510.05750.4302-60.57471.5094-33.8132
182.35630.3799-0.03161.224-0.20532.3289-0.09960.35960.145-0.08150.18150.227-0.2577-0.3884-0.08980.46590.0857-0.05990.59980.06850.2413-46.660624.7965-60.0823
193.20630.02131.99741.48160.16592.1676-0.1420.1570.0982-0.03170.07480.0091-0.2349-0.12640.03570.44660.0476-0.03940.47940.02630.1864-36.805220.2741-49.4686
206.30933.25784.86291.78243.15678.74730.16310.9786-1.3602-0.5742-0.165-0.81061.47570.9425-0.12170.71340.13920.02320.63-0.12490.409-26.1186.9353-51.8332
212.551-1.23732.26221.4304-0.85422.4332-0.22260.09620.28310.0577-0.0181-0.1615-0.3020.03030.21770.40180.0424-0.04120.40630.05790.219-18.644116.9117-36.8173
224.0124-1.03890.85590.6237-0.20810.33410.43990.0452-0.4235-0.59290.18121.53780.0361-0.2176-0.41450.65590.1221-0.3181.06610.30911.73749.135229.8517-56.532
236.4966-1.95051.07311.7764-1.99422.51760.0561-0.1865-0.214-0.02320.14121.2953-0.166-0.5620.00890.37850.1106-0.00950.74560.10380.86722.903724.9078-45.0114
241.8072-0.3610.67412.7826-0.81263.13520.1388-0.39040.10950.37030.08870.7843-0.1079-0.5646-0.22870.45140.06930.08960.69890.10780.521332.118618.9117-36.4592
253.9733-0.33150.76553.59930.31142.0422-0.6510.07610.8080.66380.15870.1809-0.9719-0.52970.25390.52650.1998-0.03410.50470.06790.397945.095919.0948-27.8013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 162 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 185 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 205 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 226 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 255 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 283 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 284 through 321 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 322 through 342 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 343 through 368 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 369 through 387 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 132 through 162 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 205 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 206 through 226 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 227 through 283 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 284 through 309 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 310 through 368 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 369 through 387 )B0
18X-RAY DIFFRACTION18chain 'C' and (resid 133 through 205 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 206 through 255 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 256 through 273 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 274 through 388 )C0
22X-RAY DIFFRACTION22chain 'D' and (resid 133 through 236 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 237 through 292 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 293 through 368 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 369 through 389 )D0

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