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- EMDB-75712: 2-APB bound rat TRPV2, H651S/D654T/N655D -

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Basic information

Entry
Database: EMDB / ID: EMD-75712
Title2-APB bound rat TRPV2, H651S/D654T/N655D
Map data
Sample
  • Complex: homo tetramer of rat TRPV2, H541S/D654T/N655D
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 2
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: 2-aminoethyl diphenylborinate
KeywordsTRPV2 / ion channel / TRP channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / endomembrane system / calcium channel activity ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / endomembrane system / calcium channel activity / melanosome / lamellipodium / positive regulation of cold-induced thermogenesis / cell body / negative regulation of cell population proliferation / axon / neuronal cell body / cell surface / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsPumroy RP / Rocereta JA / Moiseenkova-Bell VY
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144120 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural origins of species-specific differences in TRPV2 activation.
Authors: Tabea C Fricke / Ruth A Pumroy / Julia A Rocereta / José J De Jesús-Pérez / George Oprita / Marvin J A Meyer / Christine Herzog / Frank G Echtermeyer / Kerstin Hill / Andreas Leffler / ...Authors: Tabea C Fricke / Ruth A Pumroy / Julia A Rocereta / José J De Jesús-Pérez / George Oprita / Marvin J A Meyer / Christine Herzog / Frank G Echtermeyer / Kerstin Hill / Andreas Leffler / Vera Y Moiseenkova-Bell /
Abstract: Transient receptor potential vanilloid 2 (TRPV2) is a broadly expressed ion channel implicated in diverse physiological and pathological processes. Despite strong conservation, human TRPV2 (hTRPV2) ...Transient receptor potential vanilloid 2 (TRPV2) is a broadly expressed ion channel implicated in diverse physiological and pathological processes. Despite strong conservation, human TRPV2 (hTRPV2) displays markedly reduced sensitivity to stimuli such as 2-aminoethoxydiphenyl borate (2-APB) and heat compared to rodent orthologs. Here we combine electrophysiology and cryo electron microscopy to define the basis of this species-dependent divergence. The structure of hTRPV2 is remarkably different at the voltage sensor-like domain (VSLD) compared to rodent channels and functional analyses show a graded activity profile between human, mouse and rat TRPV2 to a broad range of chemical and physical stimuli. Three residues located between S6 and the TRP domain tune this functional difference, as reciprocal substitutions exchange current phenotypes. hTRPV2 structures of this mutant reveal coupling between the mutation site and the VSLD as well as an additional binding site for 2-APB. Together, these findings define structural determinants of species-specific TRPV2 function.
History
DepositionFeb 25, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75712.png

Downloads & links

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Map

FileDownload / File: emd_75712.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 288 pix.
= 255.456 Å		0.89 Å/pix.
x 288 pix.
= 255.456 Å		0.89 Å/pix.
x 288 pix.
= 255.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.887 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.010487 - 1.774661
Average (Standard dev.)0.009471428 (±0.060542613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 255.45601 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75712_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75712_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : homo tetramer of rat TRPV2, H541S/D654T/N655D

EntireName: homo tetramer of rat TRPV2, H541S/D654T/N655D
Components
  • Complex: homo tetramer of rat TRPV2, H541S/D654T/N655D
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 2
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
  • Ligand: 2-aminoethyl diphenylborinate

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Supramolecule #1: homo tetramer of rat TRPV2, H541S/D654T/N655D

SupramoleculeName: homo tetramer of rat TRPV2, H541S/D654T/N655D / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 2

MacromoleculeName: Transient receptor potential cation channel subfamily V member 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 87.603719 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTSASSPPAF RLETSDGDEE GNAEVNKGKQ EPPPMESPFQ REDRNSSPQI KVNLNFIKRP PKNTSAPSQQ EPDRFDRDRL FSVVSRGVP EELTGLLEYL RWNSKYLTDS AYTEGSTGKT CLMKAVLNLQ DGVNACIMPL LQIDKDSGNP KPLVNAQCTD E FYQGHSAL ...String:
MTSASSPPAF RLETSDGDEE GNAEVNKGKQ EPPPMESPFQ REDRNSSPQI KVNLNFIKRP PKNTSAPSQQ EPDRFDRDRL FSVVSRGVP EELTGLLEYL RWNSKYLTDS AYTEGSTGKT CLMKAVLNLQ DGVNACIMPL LQIDKDSGNP KPLVNAQCTD E FYQGHSAL HIAIEKRSLQ CVKLLVENGA DVHLRACGRF FQKHQGTCFY FGELPLSLAA CTKQWDVVTY LLENPHQPAS LE ATDSLGN TVLHALVMIA DNSPENSALV IHMYDGLLQM GARLCPTVQL EEISNHQGLT PLKLAAKEGK IEIFRHILQR EFS GPYQPL SRKFTEWCYG PVRVSLYDLS SVDSWEKNSV LEIIAFHCKS PNRHRMVVLE PLNKLLQEKW DRLVSRFFFN FACY LVYMF IFTVVAYHQP SLDQPAIPSS KATFGESMLL LGHILILLGG IYLLLGQLWY FWRRRLFIWI SFMDSYFEIL FLLQA LLTV LSQVLRFMET EWYLPLLVLS LVLGWLNLLY YTRGFQHTGI YSVMIQKVIL RDLLRFLLVY LVFLFGFAVA LVSLSR EAR SPKAPEDNNS TVTEQPTVGQ EEEPAPYRSI LDASLELFKF TIGMGELAFQ EQLRFRGVVL LLLLAYVLLT YVLLLNM LI ALMSETVNSV ATDSWSIWKL QKAISVLEME NGYWWCRRKK HREGRLLKVG TRGDGTPDER WCFRVEEVNW AAWEKTLP T LSEDPSGPGI TGNKKNPTSK PGKNSASEED HLPLQVLQSP TETSQVAPA

UniProtKB: Transient receptor potential cation channel subfamily V member 2

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Macromolecule #2: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PEX
Molecular weightTheoretical: 522.632 Da
Chemical component information

ChemComp-PEX:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

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Macromolecule #3: 2-aminoethyl diphenylborinate

MacromoleculeName: 2-aminoethyl diphenylborinate / type: ligand / ID: 3 / Number of copies: 4 / Formula: FZ4
Molecular weightTheoretical: 225.094 Da
Chemical component information

ChemComp-FZ4:
2-aminoethyl diphenylborinate

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

20677

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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