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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


vasopressin secretion / regulation of response to osmotic stress / stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / hyperosmotic salinity response / calcium ion import into cytosol / cartilage development involved in endochondral bone morphogenesis / positive regulation of microtubule depolymerization / positive regulation of striated muscle contraction ...vasopressin secretion / regulation of response to osmotic stress / stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / hyperosmotic salinity response / calcium ion import into cytosol / cartilage development involved in endochondral bone morphogenesis / positive regulation of microtubule depolymerization / positive regulation of striated muscle contraction / hypotonic response / positive regulation of macrophage inflammatory protein 1 alpha production / positive regulation of chemokine (C-X-C motif) ligand 1 production / positive regulation of chemokine (C-C motif) ligand 5 production / cellular hypotonic salinity response / cellular hypotonic response / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cortical microtubule organization / diet induced thermogenesis / multicellular organismal-level water homeostasis / calcium ion import / positive regulation of vascular permeability / TRP channels / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / negative regulation of brown fat cell differentiation / osmosensory signaling pathway / cellular response to osmotic stress / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / energy homeostasis / microtubule polymerization / calcium ion import across plasma membrane / alpha-tubulin binding / cytoplasmic microtubule / beta-tubulin binding / monoatomic cation channel activity / response to insulin / SH2 domain binding / actin filament organization / protein kinase C binding / negative regulation of neuron projection development / filopodium / adherens junction / positive regulation of interleukin-6 production / positive regulation of JNK cascade / intracellular calcium ion homeostasis / ruffle membrane / calcium channel activity / calcium ion transmembrane transport / calcium ion transport / positive regulation of inflammatory response / actin filament binding / actin cytoskeleton organization / glucose homeostasis / cilium / cellular response to heat / lamellipodium / actin binding / positive regulation of cytosolic calcium ion concentration / growth cone / calmodulin binding / microtubule binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / apical plasma membrane / focal adhesion / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / 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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