8SRJ | pdb_00008srj

Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in the presence of EDTA, apo state

  • 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: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8SRJ

This is version 1.3 of the entry. See complete history

Literature

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

Huang, Y.Kumar, S.Lee, J.Lu, W.Du, J.

(2024) Nat Struct Mol Biol 31: 1509-1521

  • DOI: https://doi.org/10.1038/s41594-024-01316-4
  • Primary Citation Related Structures: 
    8SR7, 8SR8, 8SR9, 8SRA, 8SRB, 8SRC, 8SRD, 8SRE, 8SRF, 8SRG, 8SRH, 8SRI, 8SRJ, 8SRK

  • PubMed Abstract: 

    Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP-ribose with high open probability and an enzyme module (NUDT9-H domain) consuming ADP-ribose at a remarkably slow rate. Using time-resolved cryogenic-electron microscopy, we captured a complete series of structural snapshots of gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. The slow kinetics of the NUDT9-H enzyme module confers a self-regulatory mechanism: ADPR binding triggers NUDT9-H tetramerization, promoting channel opening, while subsequent hydrolysis reduces local ADPR, inducing channel closure. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADP-ribose hydrolase module in early species to a fully integrated component of a gating ring essential for channel activation in advanced species.


  • Organizational Affiliation
    • Van Andel Institute, Grand Rapids, MI, USA.

Macromolecule Content 

  • Total Structure Weight: 554.22 kDa 
  • Atom Count: 26,156 
  • Modeled Residue Count: 4,296 
  • Deposited Residue Count: 4,856 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRPM2 chanzyme
A, B, C, D
1,214Salpingoeca rosettaMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2UB89
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
(Subject of Investigation/LOI)

Query on CLR



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
O [auth D],
P [auth D]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20rc3_4406:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS112363
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS111031
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection