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- EMDB-44643: Cholecystokinin 1 receptor (CCK1R) sterol 7M mutant, Gq chimera (... -

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Entry
Database: EMDB / ID: EMD-44643
TitleCholecystokinin 1 receptor (CCK1R) sterol 7M mutant, Gq chimera (mGsqi) complex
Map dataMain map (best class, refinement with micelle and ScFv16 masked out), unsharpened
Sample
  • Complex: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s.
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Cholecystokinin-8
    • Protein or peptide: Cholecystokinin receptor type A
Keywordscholecystokinin / GPCR / cholesterol / mutant / MEMBRANE PROTEIN
Function / homology
Function and homology information


cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / sensory perception of chemical stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / beta-2 adrenergic receptor binding / peptide hormone receptor binding ...cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / sensory perception of chemical stimulus / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / beta-2 adrenergic receptor binding / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling / developmental growth / D1 dopamine receptor binding / Hedgehog 'off' state / forebrain development / cellular response to hormone stimulus / digestion / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / adenylate cyclase activator activity / Peptide ligand-binding receptors / axonogenesis / peptide binding / neuron migration / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / bone development / 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 / photoreceptor disc membrane / platelet aggregation / Adrenaline,noradrenaline inhibits insulin secretion / 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 / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / 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 / 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 / apical plasma membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / axon / GTPase activity / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
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 / 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
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 XLas
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsHarikumar KG / Zhao P / Cary BP / Xu X / Desai AJ / Mobbs JI / Toufaily C / Furness SGB / Christopoulos A / Belousoff MJ ...Harikumar KG / Zhao P / Cary BP / Xu X / Desai AJ / Mobbs JI / Toufaily C / Furness SGB / Christopoulos A / Belousoff MJ / Wootten D / Sexton PM / Miller LJ
Funding support United States, Australia, 4 items
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 KG / Zhao P / Cary BP / Xu X / Desai AJ / Mobbs JI / Toufaily C / Furness SGB / Christopoulos A / Belousoff MJ / Wootten D / Sexton PM / Miller LJ
History
DepositionApr 29, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44643.png

Downloads & links

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Map

FileDownload / File: emd_44643.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map (best class, refinement with micelle and ScFv16 masked out), unsharpened
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-3.1318846 - 5.222252
Average (Standard dev.)0.00082438986 (±0.10034601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44643_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Main map (best class, refinement with micelle and...

Fileemd_44643_additional_1.map
AnnotationMain map (best class, refinement with micelle and ScFv16 masked out), unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Receptor local refinement (best class), unsharpened

Fileemd_44643_additional_2.map
AnnotationReceptor local refinement (best class), unsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Consensus refinement half-map B

Fileemd_44643_additional_3.map
AnnotationConsensus refinement half-map B
Projections & Slices
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Additional map: Consensus refinement half-map A

Fileemd_44643_additional_4.map
AnnotationConsensus refinement half-map A
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Additional map: Consensus refinement map, unsharpened

Fileemd_44643_additional_5.map
AnnotationConsensus refinement map, unsharpened
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Main half map A (best class, refinement with...

Fileemd_44643_half_map_1.map
AnnotationMain half map A (best class, refinement with micelle and ScFv16 masked out)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Main half map B (best class, refinement with...

Fileemd_44643_half_map_2.map
AnnotationMain half map B (best class, refinement with micelle and ScFv16 masked out)
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chime...

EntireName: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s.
Components
  • Complex: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s.
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Cholecystokinin-8
    • Protein or peptide: Cholecystokinin receptor type A

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Supramolecule #1: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chime...

SupramoleculeName: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Single-chain fragment variable 16 (ScFv16) was included in the complex but left unmodeled.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
type: protein_or_peptide / ID: 1
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
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.144971 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHHHGC TLSAEDKAAV ERSKMIDRNL REDGEKARRT LRLLLLGADN SGKSTIVKQM RILHGGSGGS GGTSGIFETK FQVDKVNFH MFDVGGQRDE RRKWIQCFND VTAIIFVVDS SDYNRLQEAL NDFKSIWNNR WLRTISVILF LNKQDLLAEK V LAGKSKIE ...String:
HHHHHHHHGC TLSAEDKAAV ERSKMIDRNL REDGEKARRT LRLLLLGADN SGKSTIVKQM RILHGGSGGS GGTSGIFETK FQVDKVNFH MFDVGGQRDE RRKWIQCFND VTAIIFVVDS SDYNRLQEAL NDFKSIWNNR WLRTISVILF LNKQDLLAEK V LAGKSKIE DYFPEFARYT TPEDATPEPG EDPRVTRAKY FIRKEFVDIS TASGDGRHIC YPHFTCAVDT ENARRIFNDC KD IILQMNL REYNLV

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.413863 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Cholecystokinin-8

MacromoleculeName: Cholecystokinin-8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.142262 KDa
SequenceString:
D(TYS)MGWMDF(NH2)

UniProtKB: Cholecystokinin

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Macromolecule #5: Cholecystokinin receptor type A

MacromoleculeName: Cholecystokinin receptor type A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.69475 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DVVDSLLVNG SNITPPCELG LENETLFCLD QPRPSKEWQP AVQILLYSLI FLLSVLGNTL VITVLIRNKR MRTVTNIFLL SLAVSDLML CLFCMPFNLI PNLLKDFIFG SAVCKTTTYF MGTSVSVSTL NLVAIALERY SAICKPLQSR VWQTKSHALK V IAATWCLS ...String:
DVVDSLLVNG SNITPPCELG LENETLFCLD QPRPSKEWQP AVQILLYSLI FLLSVLGNTL VITVLIRNKR MRTVTNIFLL SLAVSDLML CLFCMPFNLI PNLLKDFIFG SAVCKTTTYF MGTSVSVSTL NLVAIALERY SAICKPLQSR VWQTKSHALK V IAATWCLS FTIMTPYPIY SNLVPFTKNN NQTANMCRFL LPNDVMQQSW HTFLLLLLFF IPGVVMAVAY GLISLELYQG IK FEASQKK SAKERKPSTT SSGKYEDSDG CYLQKTRPPR KLELRQLSTG SSSRANRIRS NSSAANLMAK KRVIRMLIVI VVL FFLCWM PIFSANAWRA YDTASAERRL SGTPISFILL LSYTSSCVNP IIYCFMNKRF RLGFMATFPC CPNPGPPGAR GEVG EEEEG GTTGASLSRF SYSHMSASVP PQ

UniProtKB: Cholecystokinin receptor type A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR / Details: Gold coated. Negative polarity glow discharge.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6878 / Average electron dose: 60.0 e/Å2

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Image processing

Particle selectionNumber selected: 3644147
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 279231
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7mby


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9bkk:
Cholecystokinin 1 receptor (CCK1R) sterol 7M mutant, Gq chimera (mGsqi) complex

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