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- PDB-9bkj: Cholecystokinin 1 receptor (CCK1R) Y140A mutant, Gq chimera (mGsq... -

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Basic information

Entry
Database: PDB / ID: 9bkj
TitleCholecystokinin 1 receptor (CCK1R) Y140A mutant, Gq chimera (mGsqi) complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Cholecystokinin receptor type A
  • Cholecystokinin-8
KeywordsMEMBRANE PROTEIN / cholecystokinin / GPCR / cholesterol / mutant
Function / homology
Function and homology information


cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / neuropeptide hormone activity / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling / hair follicle placode formation ...cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / neuropeptide hormone activity / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / intracellular transport / Adenylate cyclase inhibitory pathway / D1 dopamine receptor binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / positive regulation of cAMP-mediated signaling / D2 dopamine receptor binding / Hedgehog 'off' state / G protein-coupled serotonin receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to forskolin / regulation of mitotic spindle organization / forebrain development / cellular response to hormone stimulus / digestion / activation of adenylate cyclase activity / adenylate cyclase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / axonogenesis / trans-Golgi network membrane / Regulation of insulin secretion / G protein-coupled receptor binding / peptide binding / neuron migration / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / cognition / photoreceptor disc membrane / response to peptide hormone / platelet aggregation / Adrenaline,noradrenaline inhibits insulin secretion / positive regulation of GTPase activity / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / GDP binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / sensory perception of smell / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / positive regulation of cold-induced thermogenesis / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway
Similarity search - Function
Cholecystokinin-like / Gastrin/cholecystokinin peptide hormone / Gastrin/cholecystokinin, conserved site / Gastrin/cholecystokinin family / Gastrin / cholecystokinin family signature. / gastrin / cholecystokinin / caerulein family / Cholecystokinin receptor type A / Cholecystokinin A receptor, N-terminal / Cholecystokinin A receptor, N-terminal domain superfamily / Cholecystokinin A receptor, N-terminal ...Cholecystokinin-like / Gastrin/cholecystokinin peptide hormone / Gastrin/cholecystokinin, conserved site / Gastrin/cholecystokinin family / Gastrin / cholecystokinin family signature. / gastrin / cholecystokinin / caerulein family / Cholecystokinin receptor type A / Cholecystokinin A receptor, N-terminal / Cholecystokinin A receptor, N-terminal domain superfamily / Cholecystokinin A receptor, N-terminal / Cholecystokinin receptor / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AMINO GROUP / Cholecystokinin / Cholecystokinin receptor type A / 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 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsCary, B.P. / Harikumar, K.G. / Zhao, P. / Desai, A.J. / Mobbs, J.M. / Toufaily, C. / Furness, S.G.B. / Christopoulos, A. / Belousoff, M.J. / Wootten, D. ...Cary, B.P. / Harikumar, K.G. / Zhao, P. / Desai, A.J. / Mobbs, J.M. / Toufaily, C. / Furness, S.G.B. / Christopoulos, A. / Belousoff, M.J. / Wootten, D. / Sexton, P.M. / Miller, L.J.
Funding support United States, Australia, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141003 United States
National Health and Medical Research Council (NHMRC, Australia)1154434 Australia
National Health and Medical Research Council (NHMRC, Australia)1155302 Australia
Australian Research Council (ARC)FT180100543 Australia
CitationJournal: To Be Published
Title: Cholesterol-dependent dynamic changes in the conformation of the type 1 cholecystokinin receptor affect ligand binding and G protein coupling
Authors: Harikumar, K.G. / Zhao, P. / Cary, B.P. / Xu, X. / Desai, A.J. / Mobbs, J.I. / Toufaily, C. / Furness, S.G.B. / Christopoulos, A. / Belousoff, M.J. / Wootten, D. / Sexton, P.M. / Miller, L.J.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
P: Cholecystokinin-8
R: Cholecystokinin receptor type A
A: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7576
Polymers121,7415
Non-polymers161
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules BGA

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


Mass: 37413.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 6375.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768
#5: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-inhibiting G alpha protein / Adenylate cyclase-stimulating G alpha protein


Mass: 29144.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1, GNAS, GNAS1, GSP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63096, UniProt: P63092

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Protein/peptide / Protein / Non-polymers , 3 types, 3 molecules PR

#3: Protein/peptide Cholecystokinin-8 / / CCK8


Mass: 1144.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06307
#4: Protein Cholecystokinin receptor type A / CCK-A receptor / CCK-AR / Cholecystokinin-1 receptor / CCK1-R


Mass: 47662.770 Da / Num. of mol.: 1 / Mutation: Y140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCKAR, CCKRA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32238
#6: Chemical ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of CCK1R (Y140A mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s.
Type: COMPLEX
Details: Single-chain fragment variable 16 (ScFv16) was included in the complex but left unmodeled.
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.150 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA, negative polarity / Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5884

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7.6particle selection
2EPUimage acquisition
4CTFFIND4.1.4CTF correction
9cryoSPARC4.1.2initial Euler assignment
10cryoSPARC4.1.2final Euler assignment
12cryoSPARC4.1.23D reconstruction
13PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3580372
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279231 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7MBY

7mby


Accession code: 7MBY / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066976
ELECTRON MICROSCOPYf_angle_d1.0439477
ELECTRON MICROSCOPYf_dihedral_angle_d7.533954
ELECTRON MICROSCOPYf_chiral_restr0.0561116
ELECTRON MICROSCOPYf_plane_restr0.0071188

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