8SRK

Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in the presence of Ca and ADP-ribose

PDB DOI: https://doi.org/10.2210/pdb8SRK/pdb
EM Map EMD-40734: 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: 4.14 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: 556.77 kDa
Atom Count: 27,328
Modelled Residue Count: 4,284
Deposited Residue Count: 4,856
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, C, D	1,214	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 K [auth B] SDF format, chain Q [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth D]	E [auth A], K [auth B], Q [auth C], Y [auth D]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain Y [auth D]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C]	BA [auth D] H [auth A] I [auth A] J [auth A] N [auth B] BA [auth D], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], V [auth C], W [auth D], X [auth D]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Z [auth D] SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B]	AA [auth D] F [auth A] G [auth A] L [auth B] M [auth B] AA [auth D], F [auth A], G [auth A], L [auth B], M [auth B], R [auth C], S [auth C], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.14 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20rc3_4406:

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