6PUS

Human TRPM2 bound to ADPR and calcium

PDB DOI: https://doi.org/10.2210/pdb6PUS/pdb
EM Map EMD-20480: EMDB EMDataResource

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

Deposited: 2019-07-18 Released: 2019-09-25
Deposition Author(s): Du, J., Lu, W., Huang, Y.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel.

Huang, Y., Roth, B., Lu, W., Du, J.

(2019) Elife 8

PubMed: 31513012 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.7554/eLife.50175
Primary Citation of Related Structures:
6PUO, 6PUR, 6PUS, 6PUU

PubMed Abstract:
TRPM2 is critically involved in diverse physiological processes including core temperature sensing, apoptosis, and immune response. TRPM2's activation by Ca ²⁺ and ADP ribose (ADPR), an NAD ⁺-metabolite produced under oxidative stress and neurodegenerative conditions, suggests a role in neurological disorders. We provide a central concept between triple-site ligand binding and the channel gating of human TRPM2. We show consecutive structural rearrangements and channel activation of TRPM2 induced by binding of ADPR in two indispensable locations, and the binding of Ca ²⁺ in the transmembrane domain. The 8-Br-cADPR-an antagonist of cADPR-binds only to the MHR1/2 domain and inhibits TRPM2 by stabilizing the channel in an apo-like conformation. We conclude that MHR1/2 acts as a orthostatic ligand-binding site for TRPM2. The NUDT9-H domain binds to a second ADPR to assist channel activation in vertebrates, but not necessary in invertebrates. Our work provides insights into the gating mechanism of human TRPM2 and its pharmacology.

Organizational Affiliation

Van Andel Institute, Grand Rapids, United States.

Macromolecule Content

Total Structure Weight: 693.76 kDa
Atom Count: 37,380
Modelled Residue Count: 5,224
Deposited Residue Count: 6,048
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 2	A, B [auth C], C [auth D], D [auth B]	1,512	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O94759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APR Query on APR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	E [auth A] F [auth A] H [auth C] I [auth C] K [auth D] E [auth A], F [auth A], H [auth C], I [auth C], K [auth D], L [auth D], N [auth B], O [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth B] Focus chain O [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain P [auth B]	G [auth A], J [auth C], M [auth D], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain P [auth B]