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- PDB-6bwj: Crystal structure of the TRPV2 ion channel in complex with RTx -

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Basic information

Entry
Database: PDB / ID: 6bwj
TitleCrystal structure of the TRPV2 ion channel in complex with RTx
ComponentsTransient receptor potential cation channel subfamily V member 2
KeywordsMEMBRANE PROTEIN / Ion Channel / TRPV channel / heat sensor / temperature sensing ion channel / Ca2+ channel
Function / homology
Function and homology information


growth cone membrane / response to temperature stimulus / positive regulation of calcium ion import / positive regulation of axon extension / axonal growth cone / calcium channel activity / cell body / positive regulation of cold-induced thermogenesis / cell surface / identical protein binding
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / 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
resiniferatoxin / Transient receptor potential cation channel subfamily V member 2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZubcevic, L. / Le, S. / Yang, H. / Lee, S.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R35NS097241 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Conformational plasticity in the selectivity filter of the TRPV2 ion channel.
Authors: Zubcevic, L. / Le, S. / Yang, H. / Lee, S.Y.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 2
B: Transient receptor potential cation channel subfamily V member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,5486
Polymers175,2112
Non-polymers1,3384
Water0
1
A: Transient receptor potential cation channel subfamily V member 2
B: Transient receptor potential cation channel subfamily V member 2
hetero molecules

A: Transient receptor potential cation channel subfamily V member 2
B: Transient receptor potential cation channel subfamily V member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,09712
Polymers350,4224
Non-polymers2,6758
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area20810 Å2
ΔGint-211 kcal/mol
Surface area107130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.054, 121.226, 185.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-801-

CA

21B-802-

CA

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Components

#1: Protein Transient receptor potential cation channel subfamily V member 2


Mass: 87605.406 Da / Num. of mol.: 2 / Mutation: F470S, L505M, L508T, Q528E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: TRPV2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1SNM3
#2: Chemical ChemComp-6EU / resiniferatoxin / RTX / Resiniferatoxin


Mass: 628.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H40O9 / Comment: toxin*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: PEG 400, Calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→185.56 Å / Num. obs: 37513 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.99 / Rpim(I) all: 0.16 / Net I/σ(I): 8.6
Reflection shellResolution: 3.1→3.21 Å / Num. unique all: 3639 / CC1/2: 0.33 / Rpim(I) all: 1.67

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AN8

5an8


Resolution: 3.1→46.997 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.32
RfactorNum. reflection% reflection
Rfree0.2719 2003 5.31 %
Rwork0.2474 --
obs0.2488 37514 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→46.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 0 94 0 9398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.66513143
X-RAY DIFFRACTIONf_dihedral_angle_d12.8325603
X-RAY DIFFRACTIONf_chiral_restr0.0381528
X-RAY DIFFRACTIONf_plane_restr0.0041645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.21080.43753710.38476540X-RAY DIFFRACTION97
3.2108-3.33930.35743750.33766720X-RAY DIFFRACTION100
3.3393-3.49120.34043760.31126759X-RAY DIFFRACTION100
3.4912-3.67520.31253610.28386753X-RAY DIFFRACTION100
3.6752-3.90540.30713860.26556731X-RAY DIFFRACTION100
3.9054-4.20680.2763780.22466707X-RAY DIFFRACTION100
4.2068-4.26980.21883820.20396709X-RAY DIFFRACTION100
4.6298-5.29890.24813750.21056784X-RAY DIFFRACTION100
5.2989-6.6730.26733790.24646701X-RAY DIFFRACTION100
6.673-46.9970.2333780.22896723X-RAY DIFFRACTION100

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