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- EMDB-35922: Agonist1 and Ruthenium Red bound state of mTRPV4 -

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Basic information

Entry
Database: EMDB / ID: EMD-35922
TitleAgonist1 and Ruthenium Red bound state of mTRPV4
Map data
Sample
  • Complex: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
  • Ligand: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one
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 / cortical microtubule organization / cellular hypotonic response / TRP channels / multicellular organismal-level water homeostasis / osmosensory signaling pathway / positive regulation of vascular permeability / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / cellular response to osmotic stress / calcium ion import / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / diet induced thermogenesis / positive regulation of macrophage chemotaxis / beta-tubulin binding / microtubule polymerization / alpha-tubulin binding / monoatomic cation channel activity / cytoplasmic microtubule / energy homeostasis / SH2 domain binding / protein kinase C binding / actin filament organization / filopodium / adherens junction / response to insulin / positive regulation of JNK cascade / calcium channel activity / positive regulation of interleukin-6 production / 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 / growth cone / positive regulation of cytosolic calcium ion concentration / microtubule binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / cilium / apical plasma membrane / focal adhesion / lipid binding / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / 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: 3.88 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-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35922.png

Downloads & links

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Map

FileDownload / File: emd_35922.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0746
Minimum - Maximum-0.34810495 - 0.58150053
Average (Standard dev.)0.00016069433 (±0.014855033)
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_35922_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_35922_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 : mTRPV4 in complex with Agonist-1 and Ruthenium Red state

EntireName: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
Components
  • Complex: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
  • Ligand: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one

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Supramolecule #1: mTRPV4 in complex with Agonist-1 and Ruthenium Red state

SupramoleculeName: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin...

MacromoleculeName: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one
type: ligand / ID: 2 / Number of copies: 4 / Formula: 9QM
Molecular weightTheoretical: 448.465 Da
Chemical component information

ChemComp-9QM:
8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one

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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: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 428608
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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