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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24496 | |||||||||
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Title | Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state | |||||||||
![]() | Full sharpen map. | |||||||||
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Function / homology | ![]() positive regulation by virus of host cell division / CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / regulation of melanocyte differentiation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling ...positive regulation by virus of host cell division / CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / regulation of melanocyte differentiation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / synapse pruning / negative regulation of neuron migration / positive regulation of microglial cell migration / negative regulation of microglial cell activation / regulation of lipopolysaccharide-mediated signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / positive regulation of transforming growth factor beta1 production / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / positive regulation of I-kappaB phosphorylation / cellular response to pH / microglial cell proliferation / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / CCR chemokine receptor binding / cranial skeletal system development / positive regulation of actin filament bundle assembly / lymphocyte chemotaxis / leukocyte migration involved in inflammatory response / phototransduction, visible light / C-C chemokine receptor activity / entrainment of circadian clock / integrin activation / C-C chemokine binding / angiogenesis involved in wound healing / eosinophil chemotaxis / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / negative regulation of cell-substrate adhesion / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / action potential / neuron remodeling / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / ligand-gated ion channel signaling pathway / monocyte chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / negative regulation of tumor necrosis factor production / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / photoreceptor outer segment / cellular response to interleukin-1 / enzyme regulator activity / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of cell migration / neutrophil chemotaxis / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / G protein activity / skeletal system development / cell projection / response to ischemia / G protein-coupled receptor binding / calcium-mediated signaling / positive regulation of smooth muscle cell proliferation / microglial cell activation / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / regulation of synaptic plasticity / Activation of the phototransduction cascade / 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 / positive regulation of insulin secretion / 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 / 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 / defense response / cytokine-mediated signaling pathway / photoreceptor disc membrane / regulation of blood pressure / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Tsutsumi N / Maeda S / Qu Q / Skiniotis G / Kobilka BK / Garcia KC | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.9 KB 23.9 KB | Display Display | ![]() |
Images | ![]() | 87.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 334.5 KB | Display | ![]() |
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Full document | ![]() | 334.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rkfMC ![]() 7rkmC ![]() 7rknC ![]() 7rkxC ![]() 7rkyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Full sharpen map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : CX3CL1-US28-G11iN18-scFv16 complex
+Supramolecule #1: CX3CL1-US28-G11iN18-scFv16 complex
+Supramolecule #2: G11iN18 heterotrimer
+Supramolecule #3: scFv16
+Supramolecule #4: CX3CL1-US28
+Macromolecule #1: Guanine nucleotide-binding protein subunit alpha-11
+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: Fractalkine
+Macromolecule #6: G-protein coupled receptor homolog US28
+Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 25 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 1 s blotting before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1330 / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 58679 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7rkf: |