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- PDB-6bbj: Xenopus Tropicalis TRPV4 -

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Basic information

Entry
Database: PDB / ID: 6bbj
TitleXenopus Tropicalis TRPV4
ComponentsTransient receptor potential cation channel, subfamily V, member 4
KeywordsMETAL TRANSPORT / Ion Channel / TRP channel
Function / homology
Function and homology information


TRP channels / osmosensory signaling pathway / calcium ion import across plasma membrane / plasma membrane => GO:0005886 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDeng, Z. / Hite, R.K. / Yuan, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS099341-01A1 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA008748 United States
American Heart Association17SDG33400229 United States
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
DepositionOct 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Transient receptor potential cation channel, subfamily V, member 4
B: Transient receptor potential cation channel, subfamily V, member 4
C: Transient receptor potential cation channel, subfamily V, member 4
D: Transient receptor potential cation channel, subfamily V, member 4


Theoretical massNumber of molelcules
Total (without water)396,3514
Polymers396,3514
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18020 Å2
ΔGint-221 kcal/mol
Surface area115530 Å2

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Components

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


Mass: 99087.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: trpv4 / Production host: Pichia (fungus) / References: UniProt: F7BWY7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRPV4 / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Xenopis tropicalis TRPV4 purified in DDM and lipids
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: .30 MDa / Experimental value: NO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Source (recombinant)Organism: Pichia (fungus)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris, pH 8.01
2150 mMsodium chlorideNaClSodium chloride1
35 mMDTT1
41 mMdodecyl maltoside1
50.06 mg/ml1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine1
60.02 mg/ml-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphoethanolamine1
70.02 mg/ml1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phospho-1-rac-glycerol1
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: TRPV4 in DDM and lipids
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: 2 second blot time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 27 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1604
Image scansSampling size: 5 µm / Width: 7420 / Height: 7676 / Movie frames/image: 40 / Used frames/image: 2-20

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1.8CTF correction
7UCSF Chimeramodel fitting
9PHENIX1.12-2829model refinement
10REFMAC5.8.0158model refinement
13RELION2.1classification
14FREALIGN9.113D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 85253
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72684
Details: Refined using Frealign with reference map low-pass filtered to 6 Angstroms
Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: FSC
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319924
ELECTRON MICROSCOPYf_angle_d0.68626964
ELECTRON MICROSCOPYf_dihedral_angle_d10.42211820
ELECTRON MICROSCOPYf_chiral_restr0.0443108
ELECTRON MICROSCOPYf_plane_restr0.0053324

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