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- EMDB-60798: Cryo-EM structure of human TRPV4 intracellular domain in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-60798
TitleCryo-EM structure of human TRPV4 intracellular domain in complex with GTPase RhoA
Map data
Sample
  • Complex: Cryo-EM structure of human TRPV4 intracellular domain in complex with GTPase RhoA
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
    • Protein or peptide: Transforming protein RhoA
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsComplex / MEMBRANE PROTEIN / Hydrolase
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 / positive regulation of macrophage inflammatory protein 1 alpha production / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization ...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 / positive regulation of macrophage inflammatory protein 1 alpha production / calcium ion import into cytosol / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / 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 / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cellular hypotonic salinity response / cleavage furrow formation / regulation of neural precursor cell proliferation / cortical microtubule organization / cellular hypotonic response / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / osmosensory signaling pathway / forebrain radial glial cell differentiation / multicellular organismal-level water homeostasis / apical junction assembly / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / positive regulation of vascular permeability / RHO GTPases activate CIT / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / Sema4D induced cell migration and growth-cone collapse / cell volume homeostasis / cellular response to osmotic stress / PCP/CE pathway / RHO GTPases activate KTN1 / calcium ion import / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / TRP channels / ossification involved in bone maturation / regulation of aerobic respiration / regulation of focal adhesion assembly / apical junction complex / negative chemotaxis / cortical actin cytoskeleton / EPHA-mediated growth cone collapse / myosin binding / regulation of neuron projection development / stress fiber assembly / diet induced thermogenesis / beta-tubulin binding / positive regulation of macrophage chemotaxis / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / microtubule polymerization / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / calcium ion import across plasma membrane / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / alpha-tubulin binding
Similarity search - Function
Transient receptor potential cation channel subfamily V member 4 / Small GTPase Rho / small GTPase Rho family profile. / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...Transient receptor potential cation channel subfamily V member 4 / Small GTPase Rho / small GTPase Rho family profile. / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Rab subfamily of small GTPases / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transforming protein RhoA / Transient receptor potential cation channel subfamily V member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsYuan Z / Ruan SS / Li SL
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82425104 China
National Natural Science Foundation of China (NSFC)82150208 China
CitationJournal: To Be Published
Title: Inactivation of RhoA for hypertension treatment through a TRPV4-RhoA-RhoGDI1 axis
Authors: Wang JW / Yuan Z
History
DepositionJul 13, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60798.png

Downloads & links

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Map

FileDownload / File: emd_60798.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.72
Minimum - Maximum-3.7341025 - 5.629144
Average (Standard dev.)-0.0022576938 (±0.07585183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60798_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_60798_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human TRPV4 intracellular domain in complex ...

EntireName: Cryo-EM structure of human TRPV4 intracellular domain in complex with GTPase RhoA
Components
  • Complex: Cryo-EM structure of human TRPV4 intracellular domain in complex with GTPase RhoA
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
    • Protein or peptide: Transforming protein RhoA
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of human TRPV4 intracellular domain in complex ...

SupramoleculeName: Cryo-EM structure of human TRPV4 intracellular domain in complex with GTPase RhoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.038719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VFNRPILFDI VSRGSTADLD GLLPFLLTHK KRLTDEEFRE PSTGKTCLPK ALLNLSNGRN DTIPVLLDIA ERTGNMREFI NSPFRDIYY RGQTALHIAI ERRCKHYVEL LVAQGADVHA QARGRFFQPK DEGGYFYFGE LPLSLAACTN QPHIVNYLTE N PHKKADMR ...String:
VFNRPILFDI VSRGSTADLD GLLPFLLTHK KRLTDEEFRE PSTGKTCLPK ALLNLSNGRN DTIPVLLDIA ERTGNMREFI NSPFRDIYY RGQTALHIAI ERRCKHYVEL LVAQGADVHA QARGRFFQPK DEGGYFYFGE LPLSLAACTN QPHIVNYLTE N PHKKADMR RQDSRGNTVL HALVAIADNT RENTKFVTKM YDLLLLKCAR LFPDSNLEAV LNNDGLSPLM MAAKTGKIGI FQ HIIRREV TDEDTRHLSR KFKDWAYGPV YSSLYDLSSL DTCGEEASVL EILVYNSKIE NRHEMLAVEP INELLRDKWR KFG AVSFYI NVVSYLCAMV IFTLTAYYQP LEGTPPYPYR TTVDYLRLAG EVITLFTGVL FFFTNIKDLF MKKCPGVNSL FIDG SFQLL YFIYSVLVIV SAALYLAGIE AYLAVMVFAL VLGWMNALYF TRGLKLTGTY SIMIQKILFK DLFRFLLVYL LFMIG YASA LVSLLNPCAN MKVCNEDQTN CTVPTYPSCR DSETFSTFLL DLFKLTIGMG DLEMLSSTKY PVVFIILLVT YIILTF VLL LNMLIALMGE TVGQVSKESK HIWKLQWATT ILDIERSFPV FLRKAFRSGE MVTVGKSSDG TPDRRWCFRV DEVNWSH

UniProtKB: Transient receptor potential cation channel subfamily V member 4

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Macromolecule #2: Transforming protein RhoA

MacromoleculeName: Transforming protein RhoA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.799158 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAIRKKLVI VGDGACGKTC LLIVFSKDQF PEVYVPTVFE NYVADIEVDG KQVELALWDT AGQEDYDRLR PLSYPDTDVI LMCFSIDSP DSLENIPEKW TPEVKHFCPN VPIILVGNKK DLRNDEHTRR ELAKMKQEPV KPEEGRDMAN RIGAFGYMEC S AKTKDGVR ...String:
MAAIRKKLVI VGDGACGKTC LLIVFSKDQF PEVYVPTVFE NYVADIEVDG KQVELALWDT AGQEDYDRLR PLSYPDTDVI LMCFSIDSP DSLENIPEKW TPEVKHFCPN VPIILVGNKK DLRNDEHTRR ELAKMKQEPV KPEEGRDMAN RIGAFGYMEC S AKTKDGVR EVFEMATRAA LQARRGKKKS GCLVL

UniProtKB: Transforming protein RhoA

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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