8SRD

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

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Salpingoeca rosetta
  • Expression System: Homo sapiens
  • Mutation(s): No 

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

wwPDB Validation   3D Report Full Report


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 

  • DOI: https://doi.org/10.1038/s41594-024-01316-4
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRPM2 chanzyme
A, B, C, D
1,494Salpingoeca rosettaMutation(s): 0 
Gene Names: PTSG_05449
UniProt
Find proteins for F2UB89 (Salpingoeca rosetta (strain ATCC 50818 / BSB-021))
Go to UniProtKB:  F2UB89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APR (Subject of Investigation/LOI)
Query on APR

Download Ideal Coordinates CCD File 
E [auth A]
GA [auth C]
L [auth A]
LA [auth D]
P [auth B]
E [auth A],
GA [auth C],
L [auth A],
LA [auth D],
P [auth B],
SA [auth D],
W [auth B],
Z [auth C]
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
FA [auth C]
HA [auth C]
IA [auth C]
JA [auth D]
K [auth A]
FA [auth C],
HA [auth C],
IA [auth C],
JA [auth D],
K [auth A],
KA [auth D],
M [auth A],
N [auth A],
RA [auth D],
V [auth B],
X [auth B],
Y [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
MA [auth D],
NA [auth D],
O [auth A],
OA [auth D],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection