+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24507 | |||||||||
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Title | Binding mode of US27-Gi-scFv16 in OCL-state | |||||||||
Map data | Full sharpen map. | |||||||||
Sample |
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Function / homology | Function and homology information C-C chemokine receptor activity / C-C chemokine binding / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization ...C-C chemokine receptor activity / C-C chemokine binding / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell chemotaxis / Regulation of insulin secretion / G protein-coupled receptor binding / virion component / calcium-mediated signaling / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / 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 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / response to peptide hormone / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / 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 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / GDP binding / cellular response to prostaglandin E stimulus / 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 / Ca2+ pathway / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / immune response / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / external side of plasma membrane / GTPase activity / virus-mediated perturbation of host defense response / centrosome / synapse / protein-containing complex binding / GTP binding / nucleolus / host cell plasma membrane / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) / Human betaherpesvirus 5 / Human cytomegalovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Tsutsumi N / Jude KM / Garcia KC | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins Authors: Tsutsumi N / Maeda S / Qu Q / Voegele M / Jude KM / Suomivuori CM / Panova O / Waghray D / Kato HE / Velasco A / Dror RO / Skiniotis G / Kobilka BK / Garcia KC | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24507.map.gz | 52.9 MB | EMDB map data format | |
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Header (meta data) | emd-24507-v30.xml emd-24507.xml | 29.3 KB 29.3 KB | Display Display | EMDB header |
Images | emd_24507.png | 86.1 KB | ||
Others | emd_24507_additional_1.map.gz emd_24507_half_map_1.map.gz emd_24507_half_map_2.map.gz | 51.6 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24507 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24507 | HTTPS FTP |
-Validation report
Summary document | emd_24507_validation.pdf.gz | 1007.1 KB | Display | EMDB validaton report |
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Full document | emd_24507_full_validation.pdf.gz | 1006.7 KB | Display | |
Data in XML | emd_24507_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_24507_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24507 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24507 | HTTPS FTP |
-Related structure data
Related structure data | 7rkyMC 7rkfC 7rkmC 7rknC 7rkxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24507.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full sharpen map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8677 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Full unsharpen map.
File | emd_24507_additional_1.map | ||||||||||||
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Annotation | Full unsharpen map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A.
File | emd_24507_half_map_1.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B.
File | emd_24507_half_map_2.map | ||||||||||||
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Annotation | Half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : US27-Gi-scFv16 complex
+Supramolecule #1: US27-Gi-scFv16 complex
+Supramolecule #2: Gi heterotrimer
+Supramolecule #3: scFv16
+Supramolecule #4: US27
+Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1
+Macromolecule #2: 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 #4: Antibody fragment scFv16
+Macromolecule #5: G-protein coupled receptor homolog US27
+Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | ||||||||||
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Buffer | pH: 7.2 Component:
Details: additives: 0.01 % w/v fluorinated octyl maltoside, 0.01 % w/v fluorinated octyl maltoside + 0.1 mM GDP, or 0.05 % w/v digitonin | ||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 15 mA | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: 3 s blotting before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 4 / Number real images: 18806 / Average electron dose: 73.0 e/Å2 Details: Three of the four grids are the same as the ones used for the CL-state US27 complex (7RKX). |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 57624 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7rky: |