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- PDB-8k4o: Cryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k4o | ||||||
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Title | Cryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1 | ||||||
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![]() | VIRAL PROTEIN / Kaposi's Sarcoma Herpesvirus GPCR / KSHV-GPCR / chemokine | ||||||
Function / homology | ![]() CXCR chemokine receptor binding / C-C chemokine receptor activity / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / G protein-coupled serotonin receptor binding / enzyme activator activity / neutrophil chemotaxis ...CXCR chemokine receptor binding / C-C chemokine receptor activity / C-C chemokine binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / G protein-coupled serotonin receptor binding / enzyme activator activity / neutrophil chemotaxis / calcium-mediated signaling / growth factor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / 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 / 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 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / specific granule lumen / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / antimicrobial humoral immune response mediated by antimicrobial peptide / GPER1 signaling / chemotaxis / 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) / tertiary granule lumen / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / nervous system development / cell cortex / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / actin cytoskeleton organization / G alpha (s) signalling events / G alpha (q) signalling events / cellular response to lipopolysaccharide / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / intracellular signal transduction / inflammatory response / immune response / G protein-coupled receptor signaling pathway / cell cycle / negative regulation of cell population proliferation / cell division / lysosomal membrane / signaling receptor binding / GTPase activity / centrosome / synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å | ||||||
![]() | Liu, Y.Z. / Liu, A.J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Cryo-EM structure of Kaposi's Sarcoma Herpesvirus GPCR (KSHV-GPCR)in complex with CXCL1 Authors: Liu, Y.Z. / Liu, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.7 KB | Display | ![]() |
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PDB format | ![]() | 163.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 56.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36888MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 37881.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 6727.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 36956.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 39914.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 6001.970 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1 and Gi protein Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107180 / Symmetry type: POINT |