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- PDB-11ib: 2-APB bound human TRPV2, S651H/T654D/D655N -

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Basic information

Entry
Database: PDB / ID: 11ib
Title2-APB bound human TRPV2, S651H/T654D/D655N
ComponentsTransient receptor potential cation channel subfamily V member 2
KeywordsMEMBRANE PROTEIN / TRPV2 / ion channel / TRP channel / 2-APB
Function / homology
Function and homology information


monoatomic ion transmembrane transporter activity / growth cone membrane / response to temperature stimulus / sensory perception / positive regulation of calcium ion import / TRP channels / calcium ion import across plasma membrane / positive regulation of axon extension / monoatomic ion channel activity / axonal growth cone ...monoatomic ion transmembrane transporter activity / growth cone membrane / response to temperature stimulus / sensory perception / positive regulation of calcium ion import / TRP channels / calcium ion import across plasma membrane / positive regulation of axon extension / monoatomic ion channel activity / axonal growth cone / monoatomic cation channel activity / calcium ion transmembrane transport / calcium channel activity / melanosome / positive regulation of cold-induced thermogenesis / 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
CHOLESTEROL / 2-aminoethyl diphenylborinate / Transient receptor potential cation channel subfamily V member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsPumroy, R.P. / Rocereta, J.A. / Moiseenkova-Bell, V.Y.
Funding support United States, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 2
D: Transient receptor potential cation channel subfamily V member 2
B: Transient receptor potential cation channel subfamily V member 2
C: Transient receptor potential cation channel subfamily V member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,39516
Polymers348,0474
Non-polymers3,34712
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "D"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUALAALADB151 - 728151 - 728
d_12CLRCLRCLRCLRDH801
d_13FZ4FZ4FZ4FZ4DI802
d_14FZ4FZ4FZ4FZ4DJ803
d_21LEULEUALAALABC151 - 728151 - 728
d_22CLRCLRCLRCLRBK801
d_23FZ4FZ4FZ4FZ4BL802
d_24FZ4FZ4FZ4FZ4BM803
d_31LEULEUALAALACD151 - 728151 - 728
d_32CLRCLRCLRCLRCN801
d_33FZ4FZ4FZ4FZ4CO802
d_34FZ4FZ4FZ4FZ4CP803
d_41LEULEUALAALAAA151 - 728151 - 728
d_42CLRCLRCLRCLRAE801
d_43FZ4FZ4FZ4FZ4AF802
d_44FZ4FZ4FZ4FZ4AG803

NCS oper:
IDCodeMatrixVector
1given(-0.999999560311, -0.00010559883837, 0.000931786361727), (0.000104702064534, -0.999999531392, -0.000962420597557), (0.000931887555581, -0.000962322614435, 0.99999910276)283.729937233, 283.969850827, 0.00827184224241
2given(4.30612772346E-5, -0.999999999073, -6.47108833606E-7), (0.999999571405, 4.30618572929E-5, -0.000924843275864), (0.000924843302872, -6.07283623558E-7, 0.999999572332)283.839924659, 0.126831534181, -0.130349384957
3given(0.00239520226823, 0.999996657531, -0.000973618513821), (-0.999992662195, 0.00239810131369, 0.00298741793045), (0.00298974278094, 0.000966455899395, 0.999995063688)-0.193501806153, 283.006470256, -0.609949468255

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 2 / TrpV2 / Osm-9-like TRP channel 2 / OTRPC2 / Vanilloid receptor-like protein 1 / VRL-1


Mass: 87011.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPV2, VRL / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y5S1
#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical
ChemComp-FZ4 / 2-aminoethyl diphenylborinate


Mass: 225.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H16BNO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homo tetramer of S651H/T654D/D655N human TRPV2 bound to 2-APB
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
3PHENIX1.21.1_5286model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27806 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 75.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002417568
ELECTRON MICROSCOPYf_angle_d0.588723880
ELECTRON MICROSCOPYf_chiral_restr0.03842740
ELECTRON MICROSCOPYf_plane_restr0.00472892
ELECTRON MICROSCOPYf_dihedral_angle_d7.0472556
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BDELECTRON MICROSCOPYNCS constraints8.88730502975E-13
ens_1d_3BDELECTRON MICROSCOPYNCS constraints6.74393785318E-13
ens_1d_4BDELECTRON MICROSCOPYNCS constraints1.17611746616E-10

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