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Yorodumi- PDB-8hqc: Structure of a GPCR-G protein in complex with a natural peptide a... -
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-Basic information
Entry | Database: PDB / ID: 8hqc | ||||||
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Title | Structure of a GPCR-G protein in complex with a natural peptide agonist | ||||||
Components |
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Keywords | SIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / G protein / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information complement component C5a binding / cell proliferation in hindbrain / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / Peptide ligand-binding receptors / complement component C5a receptor activity / Regulation of Complement cascade / response to peptidoglycan / Terminal pathway of complement ...complement component C5a binding / cell proliferation in hindbrain / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / Peptide ligand-binding receptors / complement component C5a receptor activity / Regulation of Complement cascade / response to peptidoglycan / Terminal pathway of complement / membrane attack complex / G alpha (i) signalling events / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / complement receptor mediated signaling pathway / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / positive regulation of neutrophil chemotaxis / complement activation, alternative pathway / chemokine activity / dopamine receptor signaling pathway / endopeptidase inhibitor activity / positive regulation of macrophage chemotaxis / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / G protein-coupled serotonin receptor binding / complement activation, classical pathway / positive regulation of chemokine production / Neutrophil degranulation / Peptide ligand-binding receptors / neutrophil chemotaxis / muscle contraction / positive regulation of epithelial cell proliferation / Regulation of Complement cascade / astrocyte activation / G protein-coupled receptor activity / microglial cell activation / Olfactory Signaling Pathway / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / mRNA transcription by RNA polymerase II / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / cognition / 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 / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / positive regulation of angiogenesis / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / chemotaxis / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / apical part of cell / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / G alpha (s) signalling events / cytoplasmic vesicle / G alpha (q) signalling events / basolateral plasma membrane / killing of cells of another organism / Ras protein signal transduction / cell population proliferation / negative regulation of neuron apoptotic process / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å | ||||||
Authors | Saha, S. / Maharana, J. / Yadav, M.K. / Sarma, P. / Chami, M. / Banerjee, R. / Shukla, A.K. | ||||||
Funding support | India, 1items
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Citation | Journal: Cell(Cambridge,Mass.) / Year: 2023 Title: Structure of a GPCR-G protein in complex with a synthetic peptide agonist Authors: Saha, S. / Maharana, J. / Yadav, M.K. / Sarma, P. / Chami, M. / Banerjee, R. / Shukla, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hqc.cif.gz | 213.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hqc.ent.gz | 161.1 KB | Display | PDB format |
PDBx/mmJSON format | 8hqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/8hqc ftp://data.pdbj.org/pub/pdb/validation_reports/hq/8hqc | HTTPS FTP |
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-Related structure data
Related structure data | 34947MC 8hptC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 44958.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The initial sequence in the sample sequence is the expression tag (absent in the coordinates): "MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDPIDNSSFEINYDHYGTMDPNI" The residues ...Details: The initial sequence in the sample sequence is the expression tag (absent in the coordinates): "MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDPIDNSSFEINYDHYGTMDPNI" The residues absent in the coordinates and present in the sample sequence belongs to disordered regions. Source: (gene. exp.) Mus musculus (house mouse) / Gene: C5ar1, C5ar, C5r1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30993 |
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#4: Protein | Mass: 8288.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P01031 |
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules BCG
#2: Protein | Mass: 27024.762 Da / Num. of mol.: 1 / Mutation: G42D,E43N,A227D,G230D,I332A,V335I Source method: isolated from a genetically manipulated source Details: This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha called the "mini G(o) alpha";Expression tag: "MGHHHHHHENLYFQGT" Residues absent in the coordinates: Disordered ...Details: This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha called the "mini G(o) alpha";Expression tag: "MGHHHHHHENLYFQGT" Residues absent in the coordinates: Disordered regions,This is a variant of Guanine nucleotide-binding protein G(o) subunit alpha called the "mini G(o) alpha";Expression tag: "MGHHHHHHENLYFQGT" Residues absent in the coordinates: Disordered regions Source: (gene. exp.) Homo sapiens (human) / Gene: GNAO1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09471 |
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#3: Protein | Mass: 38534.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Expression tag: "MHHHHHHGSSGS" / Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873 |
#5: Protein | Mass: 7861.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues absent in the coordinates: Disordered regions Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768 |
-Antibody , 1 types, 1 molecules H
#6: Antibody | Mass: 27340.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues absent in the coordinate file: Disordered regions Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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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
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173416 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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