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- PDB-6l93: X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain -

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Basic information

Entry
Database: PDB / ID: 6l93
TitleX-ray structure of the ligand-free human TRPV1 ankyrin repeat domain
ComponentsTransient receptor potential cation channel subfamily V member 1
KeywordsTRANSPORT PROTEIN / Channel domain
Function / homology
Function and homology information


chemosensory behavior / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception ...chemosensory behavior / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / thermoception / cellular response to acidic pH / dendritic spine membrane / TRP channels / diet induced thermogenesis / cellular response to alkaloid / cellular response to ATP / detection of temperature stimulus involved in sensory perception of pain / intracellularly gated calcium channel activity / behavioral response to pain / calcium ion import across plasma membrane / voltage-gated calcium channel activity / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / phosphoprotein binding / GABA-ergic synapse / calcium ion transmembrane transport / calcium channel activity / lipid metabolic process / transmembrane signaling receptor activity / sensory perception of taste / cellular response to heat / protein homotetramerization / postsynaptic membrane / calmodulin binding / cell surface receptor signaling pathway / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.47 Å
AuthorsTanaka, M. / Hayakawa, K. / Unno, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structure determination of the human TRPV1 ankyrin-repeat domain under nonreducing conditions.
Authors: Tanaka, M. / Hayakawa, K. / Ogawa, N. / Kurokawa, T. / Kitanishi, K. / Ite, K. / Matsui, T. / Mori, Y. / Unno, M.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 1
B: Transient receptor potential cation channel subfamily V member 1
C: Transient receptor potential cation channel subfamily V member 1
D: Transient receptor potential cation channel subfamily V member 1
E: Transient receptor potential cation channel subfamily V member 1
F: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)184,9996
Polymers184,9996
Non-polymers00
Water00
1
A: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)30,8331
Polymers30,8331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.228, 167.414, 112.632
Angle α, β, γ (deg.)90.000, 108.375, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 1 / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1


Mass: 30833.143 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV1, VR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NER1

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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: 4.46 Å3/Da / Density % sol: 72.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.125 M sodium citrate (pH 5.0), 5% PEG 8000, 2.5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.47→32.95 Å / Num. obs: 19438 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 179.57 Å2 / CC1/2: 0.993 / Rsym value: 0.098 / Net I/σ(I): 6.4
Reflection shellResolution: 4.47→4.63 Å / Num. unique obs: 4678 / CC1/2: 0.817

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PNN

2pnn


Resolution: 4.47→32.95 Å / SU ML: 0.5466 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.6591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 961 4.95 %
Rwork0.2202 18462 -
obs0.2227 19423 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 184.71 Å2
Refinement stepCycle: LAST / Resolution: 4.47→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11819 0 0 0 11819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001711998
X-RAY DIFFRACTIONf_angle_d0.480516238
X-RAY DIFFRACTIONf_chiral_restr0.03521924
X-RAY DIFFRACTIONf_plane_restr0.00262083
X-RAY DIFFRACTIONf_dihedral_angle_d1.96417312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.47-4.710.33541500.26392629X-RAY DIFFRACTION99.78
4.71-50.33271320.25432640X-RAY DIFFRACTION99.75
5-5.380.31481480.26542671X-RAY DIFFRACTION99.96
5.38-5.920.34831270.2692679X-RAY DIFFRACTION99.86
5.92-6.770.28131360.25022623X-RAY DIFFRACTION99.6
6.77-8.510.25831280.20332638X-RAY DIFFRACTION97.91
8.51-32.950.21581400.18152582X-RAY DIFFRACTION95.14

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