+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-24501 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of CX3CL1-US28-Gi-scFv16 in OC-state | |||||||||
![]() | Full sharpen map. | |||||||||
![]() |
| |||||||||
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 / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / lymphocyte chemotaxis ...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 / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / lymphocyte chemotaxis / 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 / positive regulation of transforming growth factor beta1 production / positive regulation of I-kappaB phosphorylation / microglial cell proliferation / CCR chemokine receptor binding / positive regulation of actin filament bundle assembly / C-C chemokine receptor activity / leukocyte migration involved in inflammatory response / C-C chemokine binding / integrin activation / angiogenesis involved in wound healing / eosinophil chemotaxis / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / negative regulation of cell-substrate adhesion / chemokine activity / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / neuron remodeling / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of apoptotic signaling pathway / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitotic spindle organization / cellular response to forskolin / neutrophil chemotaxis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of smooth muscle cell proliferation / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of cell migration / response to ischemia / cell projection / Regulation of insulin secretion / G protein-coupled receptor binding / cell-cell adhesion / calcium-mediated signaling / microglial cell activation / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of synaptic plasticity / 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 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / defense response / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / positive regulation of neuron projection development / cytokine-mediated signaling pathway / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / positive regulation of inflammatory response / cellular response to catecholamine stimulus / neuron cellular homeostasis / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / integrin binding / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Tsutsumi N / Qu Q / Jude KM / Skiniotis G / Garcia KC | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 116.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 23.5 KB 23.5 KB | Display Display | ![]() |
Images | ![]() | 88.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rknMC ![]() 7rkfC ![]() 7rkmC ![]() 7rkxC ![]() 7rkyC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full sharpen map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : CX3CL1-US28-Gi-scFv16 complex
+Supramolecule #1: CX3CL1-US28-Gi-scFv16 complex
+Supramolecule #2: Gi heterotrimer
+Supramolecule #3: scFv16
+Supramolecule #4: CX3CL1-US28
+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: Fractalkine
+Macromolecule #6: G-protein coupled receptor homolog US28
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 30 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.2 Component:
| ||||||||||||
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. |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 4546 / Average electron dose: 83.0 e/Å2 Details: The same specimen/movie data as the C-state CX3CL1-US28-Gi-scFv16 (7RKM). |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 60976 / 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: 165000 |
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 |
---|---|
Output model | ![]() PDB-7rkn: |