+Open data
-Basic information
Entry | Database: PDB / ID: 7rkf | |||||||||
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Title | Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Viral GPCR / HCMV / cytomegalovirus / G protein complex / GDP-bound state | |||||||||
Function / homology | Function and homology information 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 ...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 / positive regulation of transforming growth factor beta1 production / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / regulation of lipopolysaccharide-mediated signaling pathway / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / chemokine receptor activity / positive regulation of I-kappaB phosphorylation / cellular response to pH / microglial cell proliferation / positive regulation of actin filament bundle assembly / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / CCR chemokine receptor binding / leukocyte migration involved in inflammatory response / entrainment of circadian clock / lymphocyte chemotaxis / phototransduction, visible light / integrin activation / eosinophil chemotaxis / angiogenesis involved in wound healing / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / negative regulation of cell-substrate adhesion / positive regulation of cell-matrix adhesion / negative regulation of interleukin-1 beta production / 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 / photoreceptor outer segment / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to interleukin-1 / enzyme regulator activity / extrinsic apoptotic signaling pathway in absence of ligand / virus-mediated perturbation of host defense response / cell chemotaxis / neutrophil chemotaxis / negative regulation of cell migration / G protein activity / positive regulation of release of sequestered calcium ion into cytosol / cell projection / skeletal system development / G protein-coupled receptor binding / response to ischemia / microglial cell activation / positive regulation of smooth muscle cell proliferation / regulation of synaptic plasticity / G-protein beta/gamma-subunit complex binding / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein activation / defense response / 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 / positive regulation of neuron projection development / ADP signalling through P2Y purinoceptor 12 / positive regulation of insulin secretion / cell-cell adhesion / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) Human cytomegalovirus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Tsutsumi, N. / Maeda, S. / Qu, Q. / Skiniotis, G. / Kobilka, B.K. / Garcia, K.C. | |||||||||
Funding support | United States, 2items
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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, K.M. / Suomivuori, C.M. / Panova, O. / Waghray, D. / Kato, H.E. / Velasco, A. / Dror, R.O. / Skiniotis, G. / Kobilka, B.K. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7rkf.cif.gz | 247.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rkf.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 7rkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/7rkf ftp://data.pdbj.org/pub/pdb/validation_reports/rk/7rkf | HTTPS FTP |
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-Related structure data
Related structure data | 24496MC 7rkmC 7rknC 7rkxC 7rkyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 41254.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNA11, GA11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29992 |
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#2: Protein | Mass: 37728.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873 |
#3: Protein | Mass: 7432.554 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768 |
-Protein , 2 types, 2 molecules LR
#5: Protein | Mass: 10013.487 Da / Num. of mol.: 1 / Fragment: UNP residues 25-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CX3CL1, FKN, NTT, SCYD1, A-152E5.2 / Production host: Homo sapiens (human) / References: UniProt: P78423 |
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#6: Protein | Mass: 42041.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: US28 / Production host: Homo sapiens (human) / References: UniProt: P69332 |
-Antibody / Non-polymers / Sugars , 3 types, 3 molecules D
#4: Antibody | Mass: 27340.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) |
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#7: Chemical | ChemComp-GDP / |
#8: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: 1 s blotting before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Calibrated magnification: 58679 X / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 67 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1330 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: Final per-particle CTF values were determined by Relion 3.1 CTF correction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 795403 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126645 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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