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- EMDB-35919: Cryo-EM structure of apo state mTRPV4 -

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Basic information

Entry
Database: EMDB / ID: EMD-35919
TitleCryo-EM structure of apo state mTRPV4
Map data
Sample
  • Complex: apo 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 / positive regulation of striated muscle contraction / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / 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 / positive regulation of striated muscle contraction / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / 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 / filopodium / adherens junction / 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: 3.59 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
DepositionApr 12, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35919.png

Downloads & links

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Map

FileDownload / File: emd_35919.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. 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: 0.118
Minimum - Maximum-0.4322137 - 0.8014913
Average (Standard dev.)0.0022206316 (±0.025804965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35919_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_35919_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 : apo state of mTRPV4

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

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Supramolecule #1: apo state of mTRPV4

SupramoleculeName: apo 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: 75.666594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APAPQPPPIL KVFNRPILFD IVSRGSTADL DGLLSFLLTH KKRLTDEEFR EPSTGKTCLP KALLNLSNGR NDTIPVLLDI AERTGNMRE FINSPFRDIY YRGQTSLHIA IERRCKHYVE LLVAQGADVH AQARGRFFQP KDEGGYFYFG ELPLSLAACT N QPHIVNYL ...String:
APAPQPPPIL KVFNRPILFD IVSRGSTADL DGLLSFLLTH KKRLTDEEFR EPSTGKTCLP KALLNLSNGR NDTIPVLLDI AERTGNMRE FINSPFRDIY YRGQTSLHIA IERRCKHYVE LLVAQGADVH AQARGRFFQP KDEGGYFYFG ELPLSLAACT N QPHIVNYL TENPHKKADM RRQDSRGNTV LHALVAIADN TRENTKFVTK MYDLLLLKCS RLFPDSNLET VLNNDGLSPL MM AAKTGKI GVFQHIIRRE VTDEDTRHLS RKFKDWAYGP VYSSLYDLSS LDTCGEEVSV LEILVYNSKI ENRHEMLAVE PIN ELLRDK WRKFGAVSFY INVVSYLCAM VIFTLTAYYQ PLEGTPPYPY RTTVDYLRLA GEVITLFTGV LFFFTSIKDL FTKK CPGVN SLFVDGSFQL LYFIYSVLVV VSAALYLAGI EAYLAVMVFA LVLGWMNALY FTRGLKLTGT YSIMIQKILF KDLFR FLLV YLLFMIGYAS ALVTLLNPCT NMKVCDEDQS NCTVPTYPAC RDSETFSAFL LDLFKLTIGM GDLEMLSSAK YPVVFI LLL VTYIILTFVL LLNMLIALMG ETVGQVSKES KHIWKLQWAT TILDIERSFP VFLRKAFRSG EMVTVGKSSD GTPDRRW CF RVDEVNWSHW NQNLGIINED PGK

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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201371
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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