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- PDB-6cmo: Rhodopsin-Gi complex -

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Entry
Database: PDB / ID: 6cmo
TitleRhodopsin-Gi complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Fab Heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • chimera protein of Soluble cytochrome b562 and Rhodopsin
KeywordsSIGNALING PROTEIN / Rhodopsin / G protein / cryo-EM / Structure
Function / homology
Function and homology information


Activation of G protein gated Potassium channels / G-protein activation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through PI3Kgamma / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (q) signalling events / G alpha (q) signalling events / Ca2+ pathway / G alpha (12/13) signalling events ...Activation of G protein gated Potassium channels / G-protein activation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through PI3Kgamma / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (q) signalling events / G alpha (q) signalling events / Ca2+ pathway / G alpha (12/13) signalling events / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (s) signalling events / G alpha (i) signalling events / G alpha (z) signalling events / Opsins / Regulation of insulin secretion / VxPx cargo-targeting to cilium / Extra-nuclear estrogen signaling / Inactivation, recovery and regulation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / Activation of the phototransduction cascade / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Olfactory Signaling Pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / ADP signalling through P2Y purinoceptor 12 / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / ADP signalling through P2Y purinoceptor 1 / G alpha (i) signalling events / G alpha (z) signalling events / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Vasopressin regulates renal water homeostasis via Aquaporins / Presynaptic function of Kainate receptors / The canonical retinoid cycle in rods (twilight vision) / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G beta:gamma signalling through BTK / G beta:gamma signalling through CDC42 / Extra-nuclear estrogen signaling / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / PLC beta mediated events / Adenylate cyclase inhibitory pathway / G-protein activation / Ca2+ pathway / Vasopressin regulates renal water homeostasis via Aquaporins / ADP signalling through P2Y purinoceptor 1 / G alpha (i) signalling events / G alpha (z) signalling events / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G beta:gamma signalling through BTK / G beta:gamma signalling through CDC42 / Extra-nuclear estrogen signaling / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (s) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / photoreceptor inner segment membrane / absorption of visible light / G protein-coupled photoreceptor activity / 11-cis retinal binding / cellular response to light stimulus / regulation of cAMP-mediated signaling / phototransduction, visible light / cardiac muscle cell apoptotic process / G protein-coupled serotonin receptor binding / Golgi-associated vesicle membrane / G-protein beta/gamma-subunit complex / sensory perception of taste / cellular response to catecholamine stimulus / positive regulation of protein localization to cell cortex / protein heterotrimerization / alkylglycerophosphoethanolamine phosphodiesterase activity / rhodopsin mediated signaling pathway / photoreceptor cell maintenance / adenylate cyclase-activating dopamine receptor signaling pathway / cell cortex region / photoreceptor outer segment membrane / G-protein beta-subunit binding / ciliary membrane / photoreceptor disc membrane / spectrin binding / regulation of mitotic spindle organization / G-protein beta/gamma-subunit complex binding / photoreceptor outer segment / negative regulation of synaptic transmission / regulation of rhodopsin mediated signaling pathway / cellular response to forskolin / heterotrimeric G-protein complex / GTPase activating protein binding
Guanine nucleotide-binding protein, beta subunit / Trp-Asp (WD) repeats profile. / GGL domain / Cytochrome b562 / Amino terminal of the G-protein receptor rhodopsin / G-protein coupled receptors family 1 signature. / Visual pigments (opsins) retinal binding site. / Trp-Asp (WD) repeats signature. / G-protein gamma subunit domain profile. / G-protein coupled receptors family 1 profile. ...Guanine nucleotide-binding protein, beta subunit / Trp-Asp (WD) repeats profile. / GGL domain / Cytochrome b562 / Amino terminal of the G-protein receptor rhodopsin / G-protein coupled receptors family 1 signature. / Visual pigments (opsins) retinal binding site. / Trp-Asp (WD) repeats signature. / G-protein gamma subunit domain profile. / G-protein coupled receptors family 1 profile. / WD domain, G-beta repeat / Trp-Asp (WD) repeats circular profile. / G-alpha domain profile. / G-protein alpha subunit / 7 transmembrane receptor (rhodopsin family) / WD40/YVTN repeat-like-containing domain superfamily / WD40 repeat / Opsin / G-protein, gamma subunit / Cytochrome b562 / Cytochrome c/b562 / G protein alpha subunit, helical insertion / G-protein gamma-like domain / WD40-repeat-containing domain superfamily / GPCR, rhodopsin-like, 7TM / WD40-repeat-containing domain / Rhodopsin, N-terminal / WD40 repeat, conserved site / G-protein beta WD-40 repeat / P-loop containing nucleoside triphosphate hydrolase / Visual pigments (opsins) retinal binding site / G-protein gamma-like domain superfamily / G-protein alpha subunit, group I / G-protein, beta subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / Rhodopsin / G protein-coupled receptor, rhodopsin-like
Rhodopsin / Soluble cytochrome b562 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Rattus norvegicus (Norway rat)
Bos taurus (cattle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKang, 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 supportUnited States , China , 4件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseDK071662United States
American Asthma FoundationUnited States
Jay and Betty Van Andel FoundationUnited States
Ministry of Science and Technology (China)2012ZX09301001 and 2012CB910403, 2013CB910600, XDB08020303, 2013ZX09507001China
CitationJournal: 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 / 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 5, 2018 / Release: Jun 20, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 20, 2018Structure modelrepositoryInitial release
1.1Sep 12, 2018Structure modelData collection / Source and taxonomyentity_src_gen_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
1.2Oct 24, 2018Structure modelData collection / Database references / Structure summaryaudit_author / citation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.3Feb 20, 2019Structure modelAuthor supporting evidence / Data collectionpdbx_audit_support_pdbx_audit_support.funding_organization
1.4Apr 17, 2019Structure modelAuthor supporting evidence / Data collectionpdbx_audit_support_pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
R: chimera protein of Soluble cytochrome b562 and Rhodopsin
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
L: Fab light chain
H: Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,8008
Polymers187,3576
Non-polymers4422
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 3 types, 3 molecules RLH

#1: Protein/peptide chimera protein of Soluble cytochrome b562 and Rhodopsin / Cytochrome b-562 / Opsin-2


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
#5: Protein/peptide Fab light chain / Fragment antigen-binding


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)
#6: Protein/peptide Fab Heavy chain / Fragment antigen-binding


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)

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#2: Protein/peptide Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha 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
#3: Protein/peptide Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


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/peptide Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


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

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Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Protein complex of Rhodopsin with Galphai / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: RECOMBINANT
Molecular weightValue: 180 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenConc.: 9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.92 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1-2575_1692: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227386 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00412812
f_angle_d1.00617376
f_dihedral_angle_d4.7037623
f_chiral_restr0.0591949
f_plane_restr0.0072214

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