7AOV | pdb_00007aov

Crystal Structure of a TRPM2 Domain

PDB DOI: https://doi.org/10.2210/pdb7AOV/pdb

Classification: SIGNALING PROTEIN
Organism(s): Danio rerio
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-15 Released: 2022-03-02
Deposition Author(s): Sander, S., Tidow, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.231 (Depositor), 0.235 (DCC)
R-Value Work:
0.188 (Depositor), 0.191 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7AOV

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

Literature

The crystal structure of TRPM2 MHR1/2 domain reveals a conserved Zn 2+ -binding domain essential for structural integrity and channel activity.

Sander, S., Pick, J., Gattkowski, E., Fliegert, R., Tidow, H.

(2022) Protein Sci 31: e4320-e4320

PubMed: 35634784 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.4320
Primary Citation Related Structures:
7AOV

PubMed Abstract:
Transient receptor potential melastatin 2 (TRPM2) is a Ca ²⁺ -permeable, nonselective cation channel involved in diverse physiological processes such as immune response, apoptosis, and body temperature sensing. TRPM2 is activated by ADP-ribose (ADPR) and 2'-deoxy-ADPR in a Ca ²⁺ -dependent manner. While two distinct binding sites exist for ADPR that exert different functions dependent on the species, the involvement of either binding site regarding the superagonistic effect of 2'-deoxy-ADPR is not clear yet. Here, we report the crystal structure of the MHR1/2 domain of TRPM2 from zebrafish (Danio rerio), and show that both ligands bind to this domain and activate the channel. We identified a so far unrecognized Zn ²⁺ -binding domain that was not resolved in previous cryo-EM structures and that is conserved in most TRPM channels. In combination with patch clamp experiments we comprehensively characterize the effect of the Zn ²⁺ -binding domain on TRPM2 activation. Our results provide insight into a conserved motif essential for structural integrity and channel activity.

Organizational Affiliation

Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.

Macromolecule Content

Total Structure Weight: 96.13 kDa
Atom Count: 6,370
Modeled Residue Count: 754
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 2	A, B	424	Danio rerio	Mutation(s): 0 Gene Names: trpm2
UniProt
Find proteins for A0A0R4IMY7 (Danio rerio) Explore A0A0R4IMY7 Go to UniProtKB: A0A0R4IMY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R4IMY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.231 (Depositor), 0.235 (DCC)
R-Value Work: 0.188 (Depositor), 0.191 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.76	α = 90
b = 188.128	β = 102.659
c = 47.773	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHELXCD	phasing
ARP/wARP	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1328

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2022-08-17
Changes: Database references
Version 1.2: 2024-11-06
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.