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- EMDB-36373: RN-1747 bound state of mTRPV4 -

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Basic information

Entry
Database: EMDB / ID: EMD-36373
TitleRN-1747 bound state of mTRPV4
Map data
Sample
  • Complex: RN-1747 bound state of mTRPV4
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
KeywordsmTRPV4 / STRUCTURAL PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / regulation of response to osmotic stress / osmosensor activity / vasopressin secretion / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / positive regulation of striated muscle contraction / positive regulation of macrophage inflammatory protein 1 alpha production ...stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / regulation of response to osmotic stress / osmosensor activity / vasopressin secretion / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / positive regulation of striated muscle contraction / positive regulation of macrophage inflammatory protein 1 alpha production / hyperosmotic salinity response / positive regulation of chemokine (C-X-C motif) ligand 1 production / positive regulation of chemokine (C-C motif) ligand 5 production / cartilage development involved in endochondral bone morphogenesis / cellular hypotonic salinity response / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cellular hypotonic response / cortical microtubule organization / TRP channels / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / osmosensory signaling pathway / cell-cell junction assembly / positive regulation of monocyte chemotactic protein-1 production / calcium ion import / cellular response to osmotic stress / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / diet induced thermogenesis / positive regulation of macrophage chemotaxis / microtubule polymerization / alpha-tubulin binding / beta-tubulin binding / monoatomic cation channel activity / energy homeostasis / cytoplasmic microtubule / SH2 domain binding / protein kinase C binding / actin filament organization / positive regulation of JNK cascade / adherens junction / filopodium / response to insulin / positive regulation of interleukin-6 production / calcium channel activity / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / actin filament binding / glucose homeostasis / lamellipodium / negative regulation of neuron projection development / cellular response to heat / positive regulation of cytosolic calcium ion concentration / growth cone / microtubule binding / calmodulin binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / cilium / apical plasma membrane / focal adhesion / lipid binding / positive regulation of gene expression / protein kinase binding / cell surface / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / identical protein 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 / 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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsZhen WX / Yang F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122040 China
CitationJournal: Cell Discov / Year: 2023
Title: Structural basis of ligand activation and inhibition in a mammalian TRPV4 ion channel.
Authors: Wenxuan Zhen / Zhijun Zhao / Shenghai Chang / Xiaoying Chen / Yangzhuoqun Wan / Fan Yang /
History
DepositionJun 1, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36373.png

Downloads & links

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Map

FileDownload / File: emd_36373.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0833
Minimum - Maximum-0.34654856 - 0.4995992
Average (Standard dev.)0.0022887075 (±0.020200808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36373_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36373_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RN-1747 bound state of mTRPV4

EntireName: RN-1747 bound state of mTRPV4
Components
  • Complex: RN-1747 bound state of mTRPV4
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4

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Supramolecule #1: RN-1747 bound state of mTRPV4

SupramoleculeName: RN-1747 bound state of mTRPV4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: Transient receptor potential cation channel subfamily V member 4
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 79.61168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFAPAPQ PPPILKVFNR PILFDIVSRG STADLDGLLS FLLTHKKRLT DEEFREPST GKTCLPKALL NLSNGRNDTI PVLLDIAERT GNMREFINSP FRDIYYRGQT SLHIAIERRC KHYVELLVAQ G ADVHAQAR ...String:
DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFAPAPQ PPPILKVFNR PILFDIVSRG STADLDGLLS FLLTHKKRLT DEEFREPST GKTCLPKALL NLSNGRNDTI PVLLDIAERT GNMREFINSP FRDIYYRGQT SLHIAIERRC KHYVELLVAQ G ADVHAQAR GRFFQPKDEG GYFYFGELPL SLAACTNQPH IVNYLTENPH KKADMRRQDS RGNTVLHALV AIADNTRENT KF VTKMYDL LLLKCSRLFP DSNLETVLNN DGLSPLMMAA KTGKIGVFQH IIRREVTDED TRHLSRKFKD WAYGPVYSSL YDL SSLDTC GEEVSVLEIL VYNSKIENRH EMLAVEPINE LLRDKWRKFG AVSFYINVVS YLCAMVIFTL TAYYQPLEGT PPYP YRTTV DYLRLAGEVI TLFTGVLFFF TSIKDLFTKK CPGVNSLFVD GSFQLLYFIY SVLVVVSAAL YLAGIEAYLA VMVFA LVLG WMNALYFTRG LKLTGTYSIM IQKILFKDLF RFLLVYLLFM IGYASALVTL LNPCTNMKVC DEDQSNCTVP TYPACR DSE TFSAFLLDLF KLTIGMGDLE MLSSAKYPVV FILLLVTYII LTFVLLLNML IALMGETVGQ VSKESKHIWK LQWATTI LD IERSFPVFLR KAFRSGEMVT VGKSSDGTPD RRWCFRVDEV NWSHWNQNLG IINEDPGK

UniProtKB: Transient receptor potential cation channel subfamily V member 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 334401
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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