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- PDB-6rmv: The crystal structure of a TRP channel peptide bound to a G prote... -

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Basic information

Entry
Database: PDB / ID: 6rmv
TitleThe crystal structure of a TRP channel peptide bound to a G protein beta gamma heterodimer
Components
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • Transient receptor potential cation channel, subfamily M, member 3
KeywordsPROTEIN BINDING / G protein / TRP Channel / Inhibitor
Function / homology
Function and homology information


new growing cell tip / retinal rod cell development / Activation of the phototransduction cascade / Olfactory Signaling Pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G alpha (z) signalling events / Glucagon-type ligand receptors ...new growing cell tip / retinal rod cell development / Activation of the phototransduction cascade / Olfactory Signaling Pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G beta:gamma signalling through BTK / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G alpha (s) signalling events / Ca2+ pathway / G alpha (12/13) signalling events / Extra-nuclear estrogen signaling / G alpha (q) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / cellular response to light stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / zinc ion transmembrane transporter activity / metal ion transport / G alpha (i) signalling events / cell tip / zinc ion transmembrane transport / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / temperature-gated ion channel activity / ADP signalling through P2Y purinoceptor 1 / TRP channels / G protein-coupled glutamate receptor signaling pathway / spectrin binding / sodium ion transport / monoatomic cation transmembrane transport / alkylglycerophosphoethanolamine phosphodiesterase activity / calcium ion import across plasma membrane / phototransduction, visible light / monoatomic cation transport / photoreceptor outer segment / monoatomic cation channel activity / phosphatidylinositol-4,5-bisphosphate binding / cardiac muscle cell apoptotic process / visual perception / protein tetramerization / calcium ion transmembrane transport / calcium channel activity / G-protein beta/gamma-subunit complex binding / intracellular protein localization / G-protein beta-subunit binding / heterotrimeric G-protein complex / myelin sheath / sensory perception of taste / retina development in camera-type eye / GTPase binding / fibroblast proliferation / protein homotetramerization / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / calmodulin binding / cell population proliferation / G protein-coupled receptor signaling pathway / axon / GTPase activity / synapse / dendrite / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum / signal transduction / plasma membrane
Similarity search - Function
TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain ...TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Ion transport domain / Ion transport protein / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Transient receptor potential cation channel subfamily M member 1 / Transient receptor potential cation channel subfamily M member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsGruss, F. / Oberwinkler, J. / Ulens, C.
Funding support2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek - VlaanderenG0C9717N
European Union665501
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The structural basis for an on-off switch controlling G beta gamma-mediated inhibition of TRPM3 channels.
Authors: 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. / ...Authors: 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.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
C: Transient receptor potential cation channel, subfamily M, member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2864
Polymers47,1943
Non-polymers921
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, binding observed with pull-down experiments, homology, homology to PDB 1XHM, surface plasmon resonance, binding observed with bio-layer interferometry (BLI) ...Evidence: assay for oligomerization, binding observed with pull-down experiments, homology, homology to PDB 1XHM, surface plasmon resonance, binding observed with bio-layer interferometry (BLI) experiments, which is conceptionally similar to surface plasmon resonance (SPR)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-48 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.860, 80.432, 113.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62874
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 8046.260 Da / Num. of mol.: 1 / Mutation: C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gng2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63213
#3: Protein/peptide Transient receptor potential cation channel, subfamily M, member 3


Mass: 1731.109 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRPM3 exon 17 - encoded residues including 2 N-terminal and 3 C-terminal flanking residues
Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q5F4S7, UniProt: Q2TV84*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 15% (w/v) polyethylene glycol 4,000, 7.5% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.94→42.52 Å / Num. obs: 31659 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 13.2
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3044 / CC1/2: 0.528 / Rpim(I) all: 0.795 / Rrim(I) all: 1.51 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.22 Å42.52 Å
Translation6.22 Å42.52 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XHM

1xhm


Resolution: 1.94→42.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.597 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1558 4.9 %RANDOM
Rwork0.1878 ---
obs0.1896 30048 99.06 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 105.39 Å2 / Biso mean: 45.023 Å2 / Biso min: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 1.94→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 6 122 3307
Biso mean--69.4 42.07 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193247
X-RAY DIFFRACTIONr_bond_other_d0.0010.022975
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9444393
X-RAY DIFFRACTIONr_angle_other_deg0.87336890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51623.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31615554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5731526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.323 105 -
Rwork0.303 2170 -
obs--97.85 %

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