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- PDB-6c8g: Crystal structure of Transient Receptor Potential (TRP) channel T... -

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Basic information

Entry
Database: PDB / ID: 6c8g
TitleCrystal structure of Transient Receptor Potential (TRP) channel TRPV4 in the presence of barium
ComponentsTransient receptor potential cation channel, subfamily V, member 4
KeywordsTRANSPORT PROTEIN / ion channal
Function / homology
Function and homology information


TRP channels / osmosensory signaling pathway / plasma membrane => GO:0005886 / calcium ion import across plasma membrane / actin filament organization / calcium channel activity / cilium / monoatomic ion channel activity
Similarity search - Function
Transient receptor potential cation channel subfamily V member 4 / Domain of unknown function DUF3447 / 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 ...Transient receptor potential cation channel subfamily V member 4 / Domain of unknown function DUF3447 / 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
: / Transient receptor potential cation channel, subfamily V, member 4
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.31 Å
AuthorsDeng, Z. / Paknejad, N. / Maksaev, G. / Sala-Rabanal, M. / Nichols, C.G. / Hite, R.K. / Yuan, P.
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM and X-ray structures of TRPV4 reveal insight into ion permeation and gating mechanisms.
Authors: Zengqin Deng / Navid Paknejad / Grigory Maksaev / Monica Sala-Rabanal / Colin G Nichols / Richard K Hite / Peng Yuan /
Abstract: The transient receptor potential (TRP) channel TRPV4 participates in multiple biological processes, and numerous TRPV4 mutations underlie several distinct and devastating diseases. Here we present ...The transient receptor potential (TRP) channel TRPV4 participates in multiple biological processes, and numerous TRPV4 mutations underlie several distinct and devastating diseases. Here we present the cryo-EM structure of Xenopus tropicalis TRPV4 at 3.8-Å resolution. The ion-conduction pore contains an intracellular gate formed by the inner helices, but lacks any extracellular gate in the selectivity filter, as observed in other TRPV channels. Anomalous X-ray diffraction analyses identify a single ion-binding site in the selectivity filter, thus explaining TRPV4 nonselectivity. Structural comparisons with other TRP channels and distantly related voltage-gated cation channels reveal an unprecedented, unique packing interface between the voltage-sensor-like domain and the pore domain, suggesting distinct gating mechanisms. Moreover, our structure begins to provide mechanistic insights to the large set of pathogenic mutations, offering potential opportunities for drug development.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: 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 1.2Apr 4, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3Oct 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2062
Polymers77,0691
Non-polymers1371
Water0
1
A: Transient receptor potential cation channel, subfamily V, member 4
hetero molecules

A: Transient receptor potential cation channel, subfamily V, member 4
hetero molecules

A: Transient receptor potential cation channel, subfamily V, member 4
hetero molecules

A: Transient receptor potential cation channel, subfamily V, member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,8248
Polymers308,2754
Non-polymers5494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_435-x-1,-y-2,z1
crystal symmetry operation3_345-y-3/2,x-1/2,z1
crystal symmetry operation4_535y+1/2,-x-3/2,z1
Buried area19640 Å2
ΔGint-241 kcal/mol
Surface area113890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.519, 165.519, 102.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1001-

BA

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Components

#1: Protein Transient receptor potential cation channel, subfamily V, member 4


Mass: 77068.680 Da / Num. of mol.: 1 / Fragment: residues 133-797 / Mutation: N516Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: trpv4 / Production host: Komagataella pastoris (fungus) / References: UniProt: F7BWY7
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba

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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: 4.62 Å3/Da / Density % sol: 73.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM MES pH6.0, 100 mM NaCl, 5.5% PEG4000, and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7106 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7106 Å / Relative weight: 1
ReflectionResolution: 6.3→20 Å / Num. obs: 3348 / % possible obs: 99.8 % / Redundancy: 9.9 % / Rpim(I) all: 0.03 / Net I/σ(I): 30.7
Reflection shellResolution: 6.3→6.52 Å / Num. unique obs: 320 / Rpim(I) all: 0.427

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BBJ

6bbj


Resolution: 6.31→20 Å / Cor.coef. Fo:Fc: 0.806 / Cor.coef. Fo:Fc free: 0.845 / SU B: 0.028 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.167 / ESU R Free: 3.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36524 303 9.4 %RANDOM
Rwork0.36964 ---
obs0.36922 2909 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.004 Å2
Baniso -1Baniso -2Baniso -3
1-5.75 Å20 Å20 Å2
2--5.75 Å20 Å2
3----11.51 Å2
Refinement stepCycle: 1 / Resolution: 6.31→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4871 0 1 0 4872
LS refinement shellResolution: 6.312→6.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 18 -
Rwork0.479 200 -
obs--100 %

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