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- PDB-3w9f: Crystal structure of the ankyrin repeat domain of chicken TRPV4 i... -

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Basic information

Entry
Database: PDB / ID: 3w9f
TitleCrystal structure of the ankyrin repeat domain of chicken TRPV4 in complex with IP3
ComponentsVanilloid receptor-related osmotically activated channel protein
KeywordsTRANSPORT PROTEIN / ankyrin repeat domain / ARD
Function / homology
Function and homology information


osmosensory signaling pathway / monoatomic cation channel activity / phosphatidylinositol binding / adherens junction / calcium channel activity / SH3 domain binding / intracellular calcium ion homeostasis / calmodulin binding / apical plasma membrane / lipid binding ...osmosensory signaling pathway / monoatomic cation channel activity / phosphatidylinositol binding / adherens junction / calcium channel activity / SH3 domain binding / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / 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: 1.9 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 / Derived calculations / Structure summary
Category: struct / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_ref_seq_dif.details ..._struct.title / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5968
Polymers117,9164
Non-polymers1,6804
Water8,305461
1
A: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8992
Polymers29,4791
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8992
Polymers29,4791
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8992
Polymers29,4791
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8992
Polymers29,4791
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Vanilloid receptor-related osmotically activated channel protein
hetero molecules

C: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7984
Polymers58,9582
Non-polymers8402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area1990 Å2
ΔGint-12 kcal/mol
Surface area24330 Å2
MethodPISA
6
B: Vanilloid receptor-related osmotically activated channel protein
hetero molecules

D: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7984
Polymers58,9582
Non-polymers8402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2040 Å2
ΔGint-13 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.094, 48.343, 132.145
Angle α, β, γ (deg.)90.000, 101.440, 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: Chemical
ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 110-120 mM sodium MES-HCl buffer pH 6.5, 1-2% PEG 4000, 11-12% MPD, 55-60 mM 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: 1.9→50 Å / Num. all: 103603 / Num. obs: 100702 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 26.43 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.37 / Num. unique all: 10249 / Rsym value: 0.619 / % possible all: 93.3

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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: 1.9→32.807 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.7707 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 29.24 / Stereochemistry target values: ML
Details: THE I3P OMIT FO-FC MAP SHOWS CLEAR POSITIVE PEAKS CORRESPONDING TO THE I3P PHOSPHATE GROUPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 2052 2.04 %Random
Rwork0.2179 ---
obs0.2185 100556 96.69 %-
all-103998 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.82 Å2 / Biso mean: 64.4097 Å2 / Biso min: 11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8015 0 96 461 8572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098364
X-RAY DIFFRACTIONf_angle_d1.25111314
X-RAY DIFFRACTIONf_chiral_restr0.081268
X-RAY DIFFRACTIONf_plane_restr0.0061450
X-RAY DIFFRACTIONf_dihedral_angle_d14.1153139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.896-1.94050.32151220.28895770589286
1.9405-1.9890.27911400.27446377651795
1.989-2.04280.27661250.25866347647294
2.0428-2.10290.2751470.24286343649094
2.1029-2.17080.24161310.22966486661797
2.1708-2.24830.24351180.2226478659696
2.2483-2.33830.24871320.21716643677597
2.3383-2.44470.29641300.21616666679698
2.4447-2.57360.25331400.21756649678999
2.5736-2.73470.24021300.22656700683099
2.7347-2.94580.24851420.2267846926100
2.9458-3.2420.24951430.216968016944100
3.242-3.71050.23471300.208468456975100
3.7105-4.67270.20571640.187867926956100
4.6727-32.81220.26441580.22256823698197
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)
11.9676-0.1875-0.80921.63790.69332.82230.0490.08560.1196-0.1221-0.06230.1775-0.0442-0.14650.07140.1430.02540.00910.0806-0.02030.2856-19.302311.8741-6.7621
22.43860.33550.66351.07670.41852.47970.1256-0.25560.32750.0765-0.22820.3325-0.1738-0.26890.04220.1719-0.02130.06070.164-0.06770.3807-10.68522.84818.6892
31.81330.53370.47962.01930.43441.88570.3153-0.4534-0.16280.4885-0.24870.03690.1341-0.07480.01620.2753-0.09740.0620.22890.04960.21582.23922.655921.8459
45.57460.7868-4.14732.97161.88325.36290.0537-0.5638-0.2405-0.06060.036-0.34930.12370.2926-0.07920.09540.0358-0.00160.2114-0.00580.3756-27.9716-15.04538.9476
51.93670.208-0.0632.0222-1.91872.26980.0774-0.1040.02620.062-0.06340.0124-0.065-0.0456-0.08540.16510.0050.01060.1629-0.0830.3692-36.5118-7.52062.736
64.0009-1.2370.57172.1887-0.7963.46070.05360.63260.3617-0.2984-0.1571-0.1671-0.0917-0.08140.16180.18970.06140.02360.2597-0.06470.3804-42.9172-2.1682-10.5003
72.9631-0.62380.01038.148-0.69861.99350.27570.6353-0.8111-0.44630.02580.23110.2709-0.0676-0.29010.20730.0161-0.09630.3308-0.11520.5407-53.6674-6.8114-11.534
83.4668-0.2075-1.77685.86240.70763.74360.48121.3693-0.1645-0.5425-0.34330.28780.43770.1658-0.11150.33010.1931-0.04360.7458-0.0260.2502-54.62171.0899-23.4899
93.7422.84123.2862.72362.52422.882-0.13530.1788-0.0834-0.1888-0.19950.26270.1984-0.31030.21070.76010.4485-0.02921.2482-0.22790.2953-59.67921.7319-33.5602
102.65511.28512.9192.2986-0.2288.46680.0346-0.3281-0.0849-0.05630.22890.24520.0255-0.7139-0.22511.01910.2857-0.1711.54550.14150.3064-48.026227.0709-65.1172
112.14290.43251.10950.48830.06871.3593-0.1186-0.17050.3146-0.13230.12710.4483-0.22-0.57570.01471.25740.2825-0.5851.72470.11630.3912-46.747526.1371-58.4958
121.01020.59980.60891.7162-1.14432.923-0.2204-0.31780.03230.29770.22070.1968-0.2127-0.6554-0.08491.33480.5481-0.39561.73970.17530.5691-48.1628.6752-49.7178
131.13360.23291.23260.99760.78051.6892-0.18150.5062-0.0419-0.1612-0.0910.03990.0997-0.0586-0.11191.13580.1461-0.37581.33730.05350.3748-33.694717.9571-52.28
142.2742-0.28490.69541.3916-1.8853.3347-0.39680.39580.2448-0.06460.10070.0305-0.2868-0.5399-0.07071.24070.4155-0.4251.0310.0629-0.0134-30.147921.3004-44.9124
154.978-3.35982.66717.5665-1.98874.8994-0.4247-0.26130.33460.34360.5032-0.0505-0.6889-0.90640.02620.7740.2562-0.17380.8243-0.00490.2695-30.713917.233-36.131
161.9471-0.45630.02742.433-0.11843.5347-0.08670.39530.3322-0.3026-0.14150.0745-0.5126-0.16260.18140.73580.1498-0.14320.55880.05090.1726-17.00715.9767-36.9359
173.1390.84513.17241.40690.84253.1941-0.14580.23510.4041-0.1649-0.1120.1084-0.44520.09310.18970.50930.12110.04220.44270.12650.3541-7.107517.2272-29.7898
182.65322.6056-0.8355.5032-0.52362.57610.26730.1075-0.5219-0.5982-0.05720.51650.076-0.1672-0.22881.33170.226-0.68911.69090.36591.45134.599931.9047-64.3198
193.4818-0.0575-1.48443.9449-0.50731.83320.3285-0.2653-0.4832-0.11850.00960.27320.00890.0737-0.18071.0960.1428-0.52321.53970.51261.3566.082131.045-57.5734
202.00060.8798-3.32495.53243.11013.213-0.0935-0.04870.24040.3620.12170.08950.01010.1948-0.02830.93020.0354-0.29761.59140.6051.46994.681233.6157-48.3918
215.28311.292.43675.26693.79365.91970.31531.2729-0.5617-0.2567-0.27460.0229-0.27310.01760.05670.72530.0971-0.27931.30940.20920.978619.09121.9484-52.1482
227.3092-2.4632-0.26361.05440.8663.0076-0.27440.38830.6916-0.2556-0.3001-0.2768-0.50480.47280.46030.82670.027-0.23361.0610.41551.113916.644429.9408-43.3884
235.75541.40422.54865.2913-0.76295.0035-0.51890.15520.3946-0.50850.17340.347-0.40520.02280.08530.57690.0604-0.23761.00370.27910.664726.2822.9201-44.4783
242.882-0.103-0.91991.50940.21533.1761-0.03470.78730.58320.1388-0.20180.0549-0.27290.11910.17530.73770.1973-0.2031.02280.14830.658832.030818.4146-36.3013
252.8181-0.12621.08522.79040.18668.2315-0.04890.74620.5937-0.16060.03660.2707-0.4810.005-0.01860.69490.1960.020.80610.3130.72745.441519.0151-28.4962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 213 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 283 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 284 through 386 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 132 through 161 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 162 through 226 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 227 through 283 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 284 through 309 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 310 through 368 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 369 through 386 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 133 through 146 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 147 through 194 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 195 through 213 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 214 through 236 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 237 through 292 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 293 through 309 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 310 through 368 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 369 through 388 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 133 through 146 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 147 through 194 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 195 through 213 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 214 through 236 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 237 through 255 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 256 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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