8SRE

Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, closed state

PDB DOI: https://doi.org/10.2210/pdb8SRE/pdb
EM Map EMD-40728: EMDB EMDataResource

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

Deposited: 2023-05-05 Released: 2024-05-15
Deposition Author(s): Huang, Y., Kumar, S., Lu, W., Du, J.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution

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

To be published.

Macromolecule Content

Total Structure Weight: 682.63 kDa
Atom Count: 42,781
Modelled Residue Count: 5,508
Deposited Residue Count: 5,976
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRPM2 chanzyme	A, B [auth D], C [auth B], D [auth C]	1,494	Salpingoeca rosetta	Mutation(s): 0 Gene Names: PTSG_05449 Membrane Entity: Yes
UniProt
Find proteins for F2UB89 (Salpingoeca rosetta (strain ATCC 50818 / BSB-021)) Explore F2UB89 Go to UniProtKB: F2UB89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2UB89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 E [auth A] SDF format, chain GA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain R [auth D] SDF format, chain SA [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth B] MOL2 format, chain E [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain R [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth B]	E [auth A] GA [auth B] L [auth A] LA [auth C] R [auth D] E [auth A], GA [auth B], L [auth A], LA [auth C], R [auth D], SA [auth C], Y [auth D], Z [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain E [auth A] Focus chain GA [auth B] Focus chain L [auth A] Focus chain LA [auth C] Focus chain R [auth D] Focus chain SA [auth C] Focus chain Y [auth D] Focus chain Z [auth B] Interactions & Density Focus chain E [auth A] Focus chain GA [auth B] Focus chain L [auth A] Focus chain LA [auth C] Focus chain R [auth D] Focus chain SA [auth C] Focus chain Y [auth D] Focus chain Z [auth B]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain RA [auth C] SDF format, chain X [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain X [auth D]	FA [auth B] HA [auth B] IA [auth B] JA [auth C] K [auth A] FA [auth B], HA [auth B], IA [auth B], JA [auth C], K [auth A], KA [auth C], M [auth A], N [auth A], P [auth D], Q [auth D], RA [auth C], X [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain FA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain RA [auth C] Focus chain X [auth D] Interactions & Density Focus chain FA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain RA [auth C] Focus chain X [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], MA [auth C], NA [auth C], O [auth A], OA [auth C], PA [auth C], QA [auth C], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS112363
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS111031
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM129547