6RMV | pdb_00006rmv

The crystal structure of a TRP channel peptide bound to a G protein beta gamma heterodimer

• PDB DOI: https://doi.org/10.2210/pdb6RMV/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2019-05-07 Released: 2020-10-14 
• Deposition Author(s): Gruss, F., Oberwinkler, J., Ulens, C.
• Funding Organization(s): Fonds Wetenschappelijk Onderzoek - Vlaanderen, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

The structural basis for an on-off switch controlling G beta gamma-mediated inhibition of TRPM3 channels.

Behrendt, M., Gruss, F., Enzeroth, R., Dembla, S., Zhao, S., Crassous, P.A., Mohr, F., Nys, M., Louros, N., Gallardo, R., Zorzini, V., Wagner, D., Economou, A., Rousseau, F., Schymkowitz, J., Philipp, S.E., Rohacs, T., Ulens, C., Oberwinkler, J.

(2020) Proc Natl Acad Sci U S A 117: 29090-29100

• PubMed: 33122432 
• DOI: https://doi.org/10.1073/pnas.2001177117
• Primary Citation Related Structures: 
  6RMV


• PubMed Abstract: 
  

  TRPM3 channels play important roles in the detection of noxious heat and in inflammatory thermal hyperalgesia. The activity of these ion channels in somatosensory neurons is tightly regulated by µ-opioid receptors through the signaling of Gβγ proteins, thereby reducing TRPM3-mediated pain. We show here that Gβγ directly binds to a domain of 10 amino acids in TRPM3 and solve a cocrystal structure of this domain together with Gβγ. Using these data and mutational analysis of full-length proteins, we pinpoint three amino acids in TRPM3 and their interacting partners in Gβ ₁ that are individually necessary for TRPM3 inhibition by Gβγ. The 10-amino-acid Gβγ-interacting domain in TRPM3 is subject to alternative splicing. Its inclusion in or exclusion from TRPM3 channel proteins therefore provides a mechanism for switching on or off the inhibitory action that Gβγ proteins exert on TRPM3 channels.

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Organizational Affiliation: 
• Institut für Physiologie und Pathophysiologie, Philipps-Universität Marburg, 35037 Marburg, Germany.
Center for Mind, Brain and Behavior (CMBB), Philipps-Universität Marburg and Justus-Liebig-Universität Giessen, 35032 Marburg, Germany.
Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium.
Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ 07103.
Switch Laboratory, VIB Center for Brain and Disease Research, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium.
Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium.
Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, 66421 Homburg, Germany.
Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium; [e-mail] [e-mail].
Institut für Physiologie und Pathophysiologie, Philipps-Universität Marburg, 35037 Marburg, Germany; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization, homology, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 47.29 kDa 
• Atom Count: 3,313 
• Modeled Residue Count: 412 
• Deposited Residue Count: 429 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A	340	Mus musculus	Mutation(s): 0  Gene Names: Gnb1
UniProt & NIH Common Fund Data Resources
Find proteins for P62874 (Mus musculus) Explore P62874  Go to UniProtKB:  P62874
IMPC:  MGI:95781

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B	74	Mus musculus	Mutation(s): 1  Gene Names: Gng2
UniProt
Find proteins for P63213 (Mus musculus) Explore P63213  Go to UniProtKB:  P63213

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel, subfamily M, member 3	C	15	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q2TV84 (Mus musculus) Explore Q2TV84  Go to UniProtKB:  Q2TV84
IMPC:  MGI:1330305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.86	α = 90
b = 80.432	β = 90
c = 113.587	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Gruss, F., Oberwinkler, J., Ulens, C.

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Funding Organization	Location	Grant Number
Fonds Wetenschappelijk Onderzoek - Vlaanderen		G0C9717N
European Union		665501

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-11-11
  Changes: Database references
• Version 1.2: 2020-11-25
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description