+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34902 | |||||||||
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Title | GPR52 with Gs and c17 | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | GPCR / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information G protein-coupled photoreceptor activity / cellular response to light stimulus / phototransduction / locomotory behavior / G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors ...G protein-coupled photoreceptor activity / cellular response to light stimulus / phototransduction / locomotory behavior / G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G beta:gamma signalling through CDC42 / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / 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 / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||
Authors | Chen B / Xu F | |||||||||
Funding support | China, 1 items
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Citation | Journal: MedComm (2020) / Year: 2023 Title: Allosteric coupling between G-protein binding and extracellular ligand binding sites in GPR52 revealed by F-NMR and cryo-electron microscopy. Authors: Yanliu Fan / Xi Lin / Benxun Pan / Bo Chen / Dongsheng Liu / Kurt Wüthrich / Fei Xu / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34902.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-34902-v30.xml emd-34902.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34902_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_34902.png | 43.6 KB | ||
Others | emd_34902_half_map_1.map.gz emd_34902_half_map_2.map.gz | 387.1 MB 387.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34902 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34902 | HTTPS FTP |
-Validation report
Summary document | emd_34902_validation.pdf.gz | 851.3 KB | Display | EMDB validaton report |
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Full document | emd_34902_full_validation.pdf.gz | 850.9 KB | Display | |
Data in XML | emd_34902_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | emd_34902_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34902 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34902 | HTTPS FTP |
-Related structure data
Related structure data | 8hmpMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34902.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.55467 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half1 map
File | emd_34902_half_map_1.map | ||||||||||||
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Annotation | half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2 map
File | emd_34902_half_map_2.map | ||||||||||||
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Annotation | half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GPR52 and Gs with C17
Entire | Name: GPR52 and Gs with C17 |
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Components |
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-Supramolecule #1: GPR52 and Gs with C17
Supramolecule | Name: GPR52 and Gs with C17 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 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: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.41693 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: MSELDQLRQE 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 |
-Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.366764 KDa |
Recombinant expression | Organism: Spodoptera (butterflies/moths) |
Sequence | String: HHHHHHGGGS DSLEFIASKL AGGGSMASNN TASIAQARKL VEQLKMEANI DRIKVSKAAA DLMAYCEAHA KEDPLLTPVP ASENPFREK KFFSAIL |
-Macromolecule #3: Nb35
Macromolecule | Name: Nb35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.054232 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV |
-Macromolecule #4: G-protein coupled receptor 52
Macromolecule | Name: G-protein coupled receptor 52 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.28652 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MNESRWTEWR ILNMSSGIVN VSERHSCPLG FGHYSVVDVC IFETVVIVLL TFLIIAGNLT VIFVFHCAPL LHHYTTSYFI QTMAYADLF VGVSCLVPTL SLLHYSTGVH ESLTCQVFGY IISVLKSVSM WCLACISVDR YLAITKPLSY NQLVTPCRLR I CIILIWIY ...String: MNESRWTEWR ILNMSSGIVN VSERHSCPLG FGHYSVVDVC IFETVVIVLL TFLIIAGNLT VIFVFHCAPL LHHYTTSYFI QTMAYADLF VGVSCLVPTL SLLHYSTGVH ESLTCQVFGY IISVLKSVSM WCLACISVDR YLAITKPLSY NQLVTPCRLR I CIILIWIY SCLIFLPSFF GWGKPGYHGD IFEWCATSWL TSAYFTGFIV CLLYAPAAFV VCFTYFHIFK ICRQHTKEIN DR RARFPSH EVDSSRETGH SPDRRYAMVL FRITSVFYML WLPYIIYFLL ESSRVLDNPT LSFLTTWLAI SNSFCNPVIY SLS NSVF |
-Macromolecule #5: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Macromolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.964734 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVDSSDYN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG K SKIEDYFP ...String: GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVDSSDYN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG K SKIEDYFP EFARYTTPED ATPEPGEDPR VTRAKYFIRD EFLRISTASG DGRHYCYPHF TCAVDTENAR RIFNDCRDII QR MHLRQYE LL |
-Macromolecule #6: N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoro...
Macromolecule | Name: N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide type: ligand / ID: 6 / Number of copies: 1 / Formula: EN6 |
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Molecular weight | Theoretical: 489.51 Da |
Chemical component information | ChemComp-EN6: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |