- EMDB-66923: Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state -
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Basic information
Entry
Database: EMDB / ID: EMD-66923
Title
Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state
Map data
Sample
Complex: CX3CL1.44-activated us28 bound to Gq trimer with scFv fiducial
Complex: Gq trimer
Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha,Guanine nucleotide-binding protein G(q) subunit alpha
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
Complex: CX3CL1.44-US28
Protein or peptide: Processed fractalkine
Protein or peptide: G-protein coupled receptor homolog US28
Complex: scFv16
Protein or peptide: antibody fragment scFv16
Ligand: GUANOSINE-5'-DIPHOSPHATE
Keywords
GPCR / G protein / SIGNALING PROTEIN
Function / homology
Function and homology information
CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / negative regulation of neuron migration / positive regulation of microglial cell migration / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of microglial cell activation ...CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / negative regulation of neuron migration / positive regulation of microglial cell migration / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of microglial cell activation / microglial cell proliferation / negative regulation of hippocampal neuron apoptotic process / positive regulation of gonadotropin secretion / autocrine signaling / phospholipase C-activating tachykinin receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / CCR chemokine receptor binding / leukocyte migration involved in inflammatory response / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of actin filament bundle assembly / regulation of platelet activation / synapse pruning / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / entrainment of circadian clock / sensory perception of itch / positive regulation of membrane depolarization / integrin activation / phototransduction, visible light / C-C chemokine binding / eosinophil chemotaxis / C-C chemokine receptor activity / positive regulation of cell-matrix adhesion / neuron cellular homeostasis / positive regulation of neuroblast proliferation / chemokine activity / leukocyte chemotaxis / Chemokine receptors bind chemokines / regulation of canonical Wnt signaling pathway / negative regulation of interleukin-1 beta production / symbiont-mediated transformation of host cell / neuron remodeling / negative regulation of interleukin-6 production / positive chemotaxis / chemoattractant activity / cell projection / glutamate receptor signaling pathway / negative regulation of apoptotic signaling pathway / negative regulation of cell-substrate adhesion / negative regulation of tumor necrosis factor production / regulation of neurogenesis / postsynaptic cytosol / photoreceptor outer segment / response to ischemia / hormone-mediated signaling pathway / cellular response to acidic pH / symbiont-mediated perturbation of host defense response / positive regulation of smooth muscle cell proliferation / GTPase activator activity / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of release of sequestered calcium ion into cytosol / mast cell degranulation / chemokine-mediated signaling pathway / calcium-mediated signaling / positive regulation of neuron projection development / cell chemotaxis / defense response / cell-cell adhesion / neuropeptide signaling pathway / response to prostaglandin E / microglial cell activation / regulation of synaptic plasticity / G protein-coupled receptor binding / integrin binding / blood coagulation / chemotaxis / cytokine-mediated signaling pathway / G-protein beta/gamma-subunit complex binding / positive regulation of inflammatory response / Olfactory Signaling Pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors Similarity search - Function
CX3C chemokine domain / G-protein alpha subunit, group Q / Chemokine receptor family / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / : / G protein alpha subunit, helical insertion ...CX3C chemokine domain / G-protein alpha subunit, group Q / Chemokine receptor family / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / : / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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. / 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
Guanine nucleotide-binding protein G(q) subunit alpha / 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 / G protein-coupled receptor homolog US28 / Fractalkine Similarity search - Component
Biological species
Homo sapiens (human) / Mus musculus (house mouse) / Cytomegalovirus
Method
single particle reconstruction / cryo EM / Resolution: 2.86 Å
Entire : CX3CL1.44-activated us28 bound to Gq trimer with scFv fiducial
Entire
Name: CX3CL1.44-activated us28 bound to Gq trimer with scFv fiducial
Components
Complex: CX3CL1.44-activated us28 bound to Gq trimer with scFv fiducial
Complex: Gq trimer
Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha,Guanine nucleotide-binding protein G(q) subunit alpha
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
Complex: CX3CL1.44-US28
Protein or peptide: Processed fractalkine
Protein or peptide: G-protein coupled receptor homolog US28
Complex: scFv16
Protein or peptide: antibody fragment scFv16
Ligand: GUANOSINE-5'-DIPHOSPHATE
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Supramolecule #1: CX3CL1.44-activated us28 bound to Gq trimer with scFv fiducial
Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine n...
Macromolecule
Name: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha,Guanine nucleotide-binding protein G(q) subunit alpha type: protein_or_peptide / ID: 1 Details: residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 ...Details: residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI,residues 1-25 MTLESIMACCLSEEAKEARRINDEI are replaced with GCTLSAEDKAAVERSKMI Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Name: G-protein coupled receptor homolog US28 / type: protein_or_peptide / ID: 6 / Details: residues 1-9 DYKDDDDA are a FLAG tag / Number of copies: 1 / Enantiomer: LEVO
Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.00039000000000000005 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: LEICA EM GP
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Electron microscopy
Microscope
TFS KRIOS
Specialist optics
Energy filter - Name: GIF Bioquantum
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11773 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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