8E6S | pdb_00008e6s

Human TRPM2 ion channel in 1 mM dADPR and Ca2+

PDB DOI: https://doi.org/10.2210/pdb8E6S/pdb
EM Map EMD-27924: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-08-23 Released: 2024-08-14
Deposition Author(s): Wang, L., Fu, T.M., Xia, S., Wu, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8E6S

This is version 1.1 of the entry. See complete history.

Literature

A unified mechanism for human TRPM2 activation, desensitization and inhibition

Wang, L., Fu, T.-M.

To be published.

Macromolecule Content

Total Structure Weight: 689.97 kDa
Atom Count: 42,336
Modeled Residue Count: 5,320
Deposited Residue Count: 6,012
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 2	A, B, C, D	1,503	Homo sapiens	Mutation(s): 0 Gene Names: TRPM2, EREG1, KNP3, LTRPC2, TRPC7 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O94759 (Homo sapiens) Explore O94759 Go to UniProtKB: O94759
PHAROS: O94759 GTEx: ENSG00000142185
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O94759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APR (Subject of Investigation/LOI) Query on APR Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], Q [auth D]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
DAT Query on DAT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], N [auth C], R [auth D]	2'-DEOXYADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₉ P₂ DAEAPNUQQAICNR-RRKCRQDMSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B]	G [auth A], K [auth B], O [auth C], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain L [auth B]	H [auth A], L [auth B], P [auth C], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-08-14
Type: Initial release
Version 1.1: 2025-05-14
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.