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- PDB-8e6r: Human TRPM2 ion channel in 1 mM dADPR -

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Basic information

Entry
Database: PDB / ID: 8e6r
TitleHuman TRPM2 ion channel in 1 mM dADPR
ComponentsTransient receptor potential cation channel subfamily M member 2
KeywordsMEMBRANE PROTEIN / TRPM2 / TRP / ADPR / ADP-ribose / NUDT9H / NUDT9 / calcium / ion channel
Function / homology
Function and homology information


mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / ligand-gated calcium channel activity / dendritic cell differentiation / zinc ion transmembrane transport / response to purine-containing compound / cellular response to temperature stimulus / regulation of filopodium assembly / response to hydroperoxide / dendritic cell chemotaxis ...mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / ligand-gated calcium channel activity / dendritic cell differentiation / zinc ion transmembrane transport / response to purine-containing compound / cellular response to temperature stimulus / regulation of filopodium assembly / response to hydroperoxide / dendritic cell chemotaxis / calcium ion transmembrane import into cytosol / TRP channels / temperature homeostasis / sodium channel activity / intracellularly gated calcium channel activity / calcium ion import across plasma membrane / tertiary granule membrane / ficolin-1-rich granule membrane / monoatomic cation channel activity / specific granule membrane / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cytoplasmic vesicle membrane / cell projection / regulation of actin cytoskeleton organization / calcium ion transmembrane transport / calcium channel activity / cellular response to hydrogen peroxide / calcium ion transport / response to heat / perikaryon / protein homotetramerization / lysosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Chem-AR6 / Transient receptor potential cation channel subfamily M member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsWang, L. / Fu, T.M. / Xia, S. / Wu, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A unified mechanism for human TRPM2 activation, desensitization and inhibition
Authors: Wang, L. / Fu, T.-M.
History
DepositionAug 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / em_admin ...chem_comp / em_admin / em_software / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _em_admin.last_update ..._chem_comp.name / _em_admin.last_update / _em_software.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
Group: Data processing / Experimental summary / Structure summary
Data content type: EM metadata / EM metadata / EM metadata / Category: em_admin / em_software / entity
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _chem_comp.name / _em_admin.last_update ..._chem_comp.name / _em_admin.last_update / _em_software.name / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)690,13912
Polymers685,6654
Non-polymers4,4758
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transient receptor potential cation channel subfamily M member 2 / Estrogen-responsive element-associated gene 1 protein / Long transient receptor potential channel 2 ...Estrogen-responsive element-associated gene 1 protein / Long transient receptor potential channel 2 / LTrpC2 / Transient receptor potential channel 7 / TrpC7 / Transient receptor potential melastatin 2


Mass: 171416.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPM2, EREG1, KNP3, LTRPC2, TRPC7 / Production host: Homo sapiens (human) / References: UniProt: O94759
#2: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2
Has ligand of interestN
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: Human TRPM2 in 1 mM ADPR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86858 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00443420
ELECTRON MICROSCOPYf_angle_d0.95859000
ELECTRON MICROSCOPYf_dihedral_angle_d8.7755904
ELECTRON MICROSCOPYf_chiral_restr0.0516604
ELECTRON MICROSCOPYf_plane_restr0.0077452

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