+Open data
-Basic information
Entry | Database: PDB / ID: 6cmo | |||||||||||||||
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Title | Rhodopsin-Gi complex | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Rhodopsin / G protein / cryo-EM / Structure | |||||||||||||||
Function / homology | Function and homology information Opsins / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / VxPx cargo-targeting to cilium / 11-cis retinal binding / G protein-coupled photoreceptor activity ...Opsins / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / VxPx cargo-targeting to cilium / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / cellular response to light stimulus / Golgi-associated vesicle membrane / thermotaxis / response to light intensity / phototransduction, visible light / detection of temperature stimulus involved in thermoception / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / photoreceptor cell maintenance / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (i) signalling events / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / alkylglycerophosphoethanolamine phosphodiesterase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / ciliary membrane / G alpha (q) signalling events / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / The canonical retinoid cycle in rods (twilight vision) / phototransduction / photoreceptor outer segment / 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 / regulation of mitotic spindle organization / cellular response to forskolin / sperm midpiece / cardiac muscle cell apoptotic process / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / photoreceptor inner segment / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / electron transport chain / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / microtubule cytoskeleton organization / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GPER1 signaling Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) Rattus norvegicus (Norway rat) Bos taurus (cattle) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
Authors | Kang, Y. / Kuybeda, O. / de Waal, P.W. / Mukherjee, S. / Van Eps, N. / Dutka, P. / Zhou, X.E. / Bartesaghi, A. / Erramilli, S. / Morizumi, T. ...Kang, Y. / Kuybeda, O. / de Waal, P.W. / Mukherjee, S. / Van Eps, N. / Dutka, P. / Zhou, X.E. / Bartesaghi, A. / Erramilli, S. / Morizumi, T. / Gu, X. / Yin, Y. / Liu, P. / Jiang, Y. / Meng, X. / Zhao, G. / Melcher, K. / Earnst, O.P. / Kossiakoff, A.A. / Subramaniam, S. / Xu, H.E. | |||||||||||||||
Funding support | United States, China, 4items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Authors: Yanyong Kang / Oleg Kuybeda / Parker W de Waal / Somnath Mukherjee / Ned Van Eps / Przemyslaw Dutka / X Edward Zhou / Alberto Bartesaghi / Satchal Erramilli / Takefumi Morizumi / Xin Gu / ...Authors: Yanyong Kang / Oleg Kuybeda / Parker W de Waal / Somnath Mukherjee / Ned Van Eps / Przemyslaw Dutka / X Edward Zhou / Alberto Bartesaghi / Satchal Erramilli / Takefumi Morizumi / Xin Gu / Yanting Yin / Ping Liu / Yi Jiang / Xing Meng / Gongpu Zhao / Karsten Melcher / Oliver P Ernst / Anthony A Kossiakoff / Sriram Subramaniam / H Eric Xu / Abstract: G-protein-coupled receptors comprise the largest family of mammalian transmembrane receptors. They mediate numerous cellular pathways by coupling with downstream signalling transducers, including the ...G-protein-coupled receptors comprise the largest family of mammalian transmembrane receptors. They mediate numerous cellular pathways by coupling with downstream signalling transducers, including the hetrotrimeric G proteins G (stimulatory) and G (inhibitory) and several arrestin proteins. The structural mechanisms that define how G-protein-coupled receptors selectively couple to a specific type of G protein or arrestin remain unknown. Here, using cryo-electron microscopy, we show that the major interactions between activated rhodopsin and G are mediated by the C-terminal helix of the G α-subunit, which is wedged into the cytoplasmic cavity of the transmembrane helix bundle and directly contacts the amino terminus of helix 8 of rhodopsin. Structural comparisons of inactive, G-bound and arrestin-bound forms of rhodopsin with inactive and G-bound forms of the β-adrenergic receptor provide a foundation to understand the unique structural signatures that are associated with the recognition of G, G and arrestin by activated G-protein-coupled receptors. | |||||||||||||||
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 | 6cmo.cif.gz | 281 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cmo.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cmo_validation.pdf.gz | 790.4 KB | Display | wwPDB validaton report |
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Full document | 6cmo_full_validation.pdf.gz | 797.7 KB | Display | |
Data in XML | 6cmo_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 6cmo_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/6cmo ftp://data.pdbj.org/pub/pdb/validation_reports/cm/6cmo | HTTPS FTP |
-Related structure data
Related structure data | 7517MC 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 ABG
#2: Protein | Mass: 40445.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63096 |
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#3: Protein | Mass: 37915.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54311 |
#4: Protein | Mass: 7563.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212 |
-Antibody , 2 types, 2 molecules LH
#5: Antibody | Mass: 23258.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect) |
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#6: Antibody | Mass: 25788.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: Bacteria Latreille et al. 1825 (Bacteria stick insect) |
-Protein / Sugars , 2 types, 2 molecules R
#1: Protein | Mass: 52385.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: cybC, RHO, OPN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P08100 |
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#7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-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 | Name: Protein complex of Rhodopsin with Galphai / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 180 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 9 mg/ml / 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 FIELD |
Image recording | Electron dose: 1.92 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1-2575_1692: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227386 / Symmetry type: POINT | ||||||||||||||||||||||||
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