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

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Basic information

Entry
Database: PDB / ID: 3jxj
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 / Transient receptor potential cation channel subfamily V member 1-4 / Ankyrin repeat-containing domain / 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 / Transient receptor potential cation channel subfamily V member 1-4 / Ankyrin repeat-containing domain / 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
PHOSPHATE ION / 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: 2.8 Å
AuthorsPhelps, C.B. / Choo, S.S. / 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 20, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1484
Polymers58,9582
Non-polymers1902
Water0
1
A: Vanilloid receptor-related osmotically activated channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5742
Polymers29,4791
Non-polymers951
Water0
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)29,5742
Polymers29,4791
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.771, 77.333, 186.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29478.891 Da / Num. of mol.: 2 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.025 M KH2PO4, 7% MPD, 7% PEG8000, and 5 mM DTT, pH 8.0, 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: Feb 14, 2006 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 14247 / % possible obs: 80.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.135 / Χ2: 1.477 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.93.10.1725100.908130.1
2.9-3.023.20.1847420.94142.3
3.02-3.153.20.20510351.173159.8
3.15-3.323.60.22113771.238179.9
3.32-3.534.50.24816091.689192.2
3.53-3.85.60.24417141.728197.7
3.8-4.187.30.20417511.802199.9
4.18-4.788.10.15517981.634199.8
4.78-6.028.20.14618061.2531100
6.02-308.10.07819051.266199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRPV4-ARD (3jxi)

3jxi


Resolution: 2.8→29.77 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 53.486 / SU ML: 0.451 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.501
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.298 710 5 %RANDOM
Rwork0.262 ---
obs0.264 14136 79.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.56 Å2 / Biso mean: 45.556 Å2 / Biso min: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3999 0 10 0 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224108
X-RAY DIFFRACTIONr_bond_other_d0.0060.022848
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9695557
X-RAY DIFFRACTIONr_angle_other_deg0.80436924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2915515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83923.177192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14915728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2051536
X-RAY DIFFRACTIONr_chiral_restr0.0610.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
X-RAY DIFFRACTIONr_mcbond_it0.4481.52534
X-RAY DIFFRACTIONr_mcbond_other0.0671.51027
X-RAY DIFFRACTIONr_mcangle_it0.87724074
X-RAY DIFFRACTIONr_scbond_it1.31431574
X-RAY DIFFRACTIONr_scangle_it2.3424.51477
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 15 -
Rwork0.295 328 -
all-343 -
obs--26.88 %
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)
16.5558-3.05611.28678.09352.479212.17520.3556-0.68870.16110.6993-0.27210.1238-0.224-0.1572-0.08360.2923-0.15290.09650.1835-0.0240.04727.9189.53778.246
27.7304-0.8516-2.60383.89592.215910.32340.1981-0.26540.0192-0.0413-0.30520.3590.1352-0.56720.10710.2011-0.0844-0.00830.20780.03250.096929.5327.76866.522
313.0084-1.9147-1.30765.16811.71589.0512-0.30270.3272-0.9097-0.01790.0251-0.17430.9259-0.35540.27770.2507-0.13710.06890.27360.00840.112535.9412.90256.689
45.8414-0.01913.04766.40390.73079.5394-0.1481-0.0344-0.70060.2501-0.39420.11731.1664-0.94220.54230.3784-0.07980.1840.459-0.10890.191537.245-2.17139.638
53.32821.4711-1.24131.37231.56646.6650.11780.02650.2486-0.0143-0.20030.1812-0.2788-0.59150.08250.31870.07320.05920.35440.12670.249140.7245.38932.086
63.93523.17941.44088.5447-0.570311.4373-0.18280.49630.2407-0.78090.28670.1580.5549-0.0896-0.10390.2737-0.10940.00620.19670.01350.048519.8311.919-23.306
76.58741.39560.0023.071-1.73497.68880.0610.0244-0.0312-0.2131-0.1178-0.02450.41520.01030.05670.3474-0.07920.01510.1188-0.02390.123218.2129.362-11.732
810.69521.9364-3.02665.4308-1.75929.1294-0.35950.1721-0.4766-0.18730.1074-0.08830.50660.00440.25210.133-0.00470.00140.1087-0.01050.088213.9126.641-2.127
92.06130.293-1.0387.38171.43136.4907-0.4469-0.1487-0.42470.23020.3390.06611.00760.49420.1080.24280.0990.07410.2430.08690.24249.601-2.22814.082
104.2694-0.7188-0.32412.035-2.97087.30330.0328-0.19450.10780.1094-0.1109-0.2090.16420.29480.07810.3150.03770.07140.20070.00670.189474.70222.379
116.84460.1087-4.29934.02550.65619.05840.30090.54940.2163-0.0507-0.17670.3687-0.4231-1.2819-0.12420.24630.02620.09180.43970.00920.162732.699.05147.329
127.9012-2.42761.55130.47949.9446-0.1658-0.29950.0875-0.01830.2768-0.2168-0.16090.729-0.11090.30750.0750.04120.1781-0.02410.143915.4489.1117.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 175
2X-RAY DIFFRACTION2A176 - 222
3X-RAY DIFFRACTION3A223 - 269
4X-RAY DIFFRACTION4A306 - 334
5X-RAY DIFFRACTION5A335 - 391
6X-RAY DIFFRACTION6B133 - 175
7X-RAY DIFFRACTION7B176 - 222
8X-RAY DIFFRACTION8B223 - 269
9X-RAY DIFFRACTION9B306 - 334
10X-RAY DIFFRACTION10B335 - 391
11X-RAY DIFFRACTION11A270 - 305
12X-RAY DIFFRACTION12B270 - 305

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