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- EMDB-35921: GSK101 bound state of mTRPV4 -

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Basic information

Entry
Database: EMDB / ID: EMD-35921
TitleGSK101 bound state of mTRPV4
Map data
Sample
  • Complex: GSK101 bound state of mTRPV4
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
  • Ligand: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazin-1-yl}-4-methyl-1-oxopentan-2-yl]-1-benzothiophene-2-carboxamide
KeywordsmTRPV4 / STRUCTURAL PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / positive regulation of striated muscle contraction / calcium ion import into cytosol / positive regulation of macrophage inflammatory protein 1 alpha production / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / hyperosmotic salinity response ...stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / positive regulation of striated muscle contraction / calcium ion import into cytosol / positive regulation of macrophage inflammatory protein 1 alpha production / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / hyperosmotic salinity response / hypotonic response / cortical microtubule organization / 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 response / regulation of response to osmotic stress / cellular hypotonic salinity response / TRP channels / osmosensory signaling pathway / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / cellular response to osmotic stress / calcium ion import / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / beta-tubulin binding / diet induced thermogenesis / microtubule polymerization / alpha-tubulin binding / cytoplasmic microtubule / energy homeostasis / monoatomic cation channel activity / SH2 domain binding / protein kinase C binding / filopodium / actin filament organization / calcium ion transmembrane transport / adherens junction / positive regulation of JNK cascade / response to insulin / calcium channel activity / cilium / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / calcium ion transport / actin filament binding / glucose homeostasis / negative regulation of neuron projection development / lamellipodium / cellular response to heat / actin binding / growth cone / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / microtubule binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / 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 / identical protein binding / metal ion 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: 3.62 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-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35921.png

Downloads & links

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Map

FileDownload / File: emd_35921.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.46623006 - 0.819864
Average (Standard dev.)0.00024997187 (±0.02175716)
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_35921_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_35921_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 : GSK101 bound state of mTRPV4

EntireName: GSK101 bound state of mTRPV4
Components
  • Complex: GSK101 bound state of mTRPV4
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
  • Ligand: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazin-1-yl}-4-methyl-1-oxopentan-2-yl]-1-benzothiophene-2-carboxamide

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Supramolecule #1: GSK101 bound state of mTRPV4

SupramoleculeName: GSK101 bound state of mTRPV4 / 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: 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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Macromolecule #2: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazi...

MacromoleculeName: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazin-1-yl}-4-methyl-1-oxopentan-2-yl]-1-benzothiophene-2-carboxamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: XQ3
Molecular weightTheoretical: 655.613 Da
Chemical component information

ChemComp-XQ3:
N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazin-1-yl}-4-methyl-1-oxopentan-2-yl]-1-benzothiophene-2-carboxamide

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

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 452263

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