[English] 日本語
Yorodumi- EMDB-44643: Cholecystokinin 1 receptor (CCK1R) sterol 7M mutant, Gq chimera (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44643 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cholecystokinin 1 receptor (CCK1R) sterol 7M mutant, Gq chimera (mGsqi) complex | |||||||||||||||
Map data | Main map (best class, refinement with micelle and ScFv16 masked out), unsharpened | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | cholecystokinin / 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 / neuropeptide hormone activity / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling ...cholecystokinin receptor activity / cholecystokinin signaling pathway / regulation of hormone secretion / neuropeptide receptor activity / sensory perception of chemical stimulus / neuropeptide hormone activity / peptide hormone receptor binding / eating behavior / peptide hormone binding / PKA activation in glucagon signalling / mu-type opioid receptor binding / developmental growth / corticotropin-releasing hormone receptor 1 binding / D1 dopamine receptor binding / Hedgehog 'off' state / beta-2 adrenergic receptor binding / forebrain development / cellular response to hormone stimulus / digestion / adenylate cyclase activator activity / Peptide ligand-binding receptors / axonogenesis / peptide binding / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / neuron migration / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / bone development / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / hormone activity / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / 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) / GTPase binding / retina development in camera-type eye / 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 / G protein-coupled receptor signaling pathway / apical plasma membrane / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.51 Å | |||||||||||||||
Authors | Harikumar 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
| |||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_44643.map.gz | 59.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-44643-v30.xml emd-44643.xml | 33.3 KB 33.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44643_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_44643.png | 73.1 KB | ||
Masks | emd_44643_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-44643.cif.gz | 7.6 KB | ||
Others | emd_44643_additional_1.map.gz emd_44643_additional_2.map.gz emd_44643_additional_3.map.gz emd_44643_additional_4.map.gz emd_44643_additional_5.map.gz emd_44643_half_map_1.map.gz emd_44643_half_map_2.map.gz | 32.2 MB 32.1 MB 59.5 MB 59.5 MB 31.9 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44643 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44643 | HTTPS FTP |
-Validation report
Summary document | emd_44643_validation.pdf.gz | 1002.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_44643_full_validation.pdf.gz | 1002.4 KB | Display | |
Data in XML | emd_44643_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_44643_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44643 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44643 | HTTPS FTP |
-Related structure data
Related structure data | 9bkkMC 9bkjC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_44643.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main map (best class, refinement with micelle and ScFv16 masked out), unsharpened | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_44643_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Main map (best class, refinement with micelle and...
File | emd_44643_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main map (best class, refinement with micelle and ScFv16 masked out), unsharpened | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Receptor local refinement (best class), unsharpened
File | emd_44643_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Receptor local refinement (best class), unsharpened | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Consensus refinement half-map B
File | emd_44643_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Consensus refinement half-map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Consensus refinement half-map A
File | emd_44643_additional_4.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Consensus refinement half-map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Consensus refinement map, unsharpened
File | emd_44643_additional_5.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Consensus refinement map, unsharpened | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Main half map A (best class, refinement with...
File | emd_44643_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main half map A (best class, refinement with micelle and ScFv16 masked out) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Main half map B (best class, refinement with...
File | emd_44643_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main half map B (best class, refinement with micelle and ScFv16 masked out) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chime...
Entire | Name: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chimera), G-beta1, G-gamma-2 and CCK8s. |
---|---|
Components |
|
-Supramolecule #1: Complex of CCK1R (sterol 7M mutant) bound to miniGs (Gq, Gi chime...
Supramolecule | Name: 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 weight | Theoretical: 150 KDa |
-Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
Macromolecule | Name: 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 weight | Theoretical: 29.144971 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: 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 weight | Theoretical: 37.413863 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: 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 weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #4: Cholecystokinin-8
Macromolecule | Name: Cholecystokinin-8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.142262 KDa |
Sequence | String: D(TYS)MGWMDF(NH2) UniProtKB: Cholecystokinin |
-Macromolecule #5: Cholecystokinin receptor type A
Macromolecule | Name: Cholecystokinin receptor type A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.69475 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.8 mg/mL |
---|---|
Buffer | pH: 7.4 |
Grid | Model: 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. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6878 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |