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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 / homologyGuanine nucleotide-binding protein, beta subunit / G-protein gamma subunit domain profile. / G-protein alpha subunit / 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. / Trp-Asp (WD) repeats profile. ...Guanine nucleotide-binding protein, beta subunit / G-protein gamma subunit domain profile. / G-protein alpha subunit / 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. / Trp-Asp (WD) repeats profile. / 7 transmembrane receptor (rhodopsin family) / G-protein coupled receptors family 1 profile. / Trp-Asp (WD) repeats circular profile. / Activation of G protein gated Potassium channels / Glucagon signaling in metabolic regulation / G-protein activation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 12 / WD domain, G-beta repeat / WD40-repeat-containing domain superfamily / Prostacyclin signalling through prostacyclin receptor / 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 / Ca2+ pathway / G-protein gamma-like 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 beta:gamma signalling through PI3Kgamma / Adrenaline,noradrenaline inhibits insulin secretion / G-protein alpha subunit, group I / VxPx cargo-targeting to cilium / ADP signalling through P2Y purinoceptor 12 / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation 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 / Inactivation, recovery and regulation of the phototransduction cascade / The canonical retinoid cycle in rods (twilight vision) / Ca2+ pathway / Glucagon-type ligand receptors / G alpha (q) signalling events / G alpha (12/13) signalling events / G beta:gamma signalling through PLC beta / G alpha (s) signalling events / ADP signalling through P2Y purinoceptor 1 / G alpha (i) signalling events / G alpha (z) signalling events / Thromboxane signalling through TP receptor / G-protein activation / Vasopressin regulates renal water homeostasis via Aquaporins / Thrombin signalling through proteinase activated receptors (PARs) / Presynaptic function of Kainate receptors / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / PLC beta mediated events / Adenylate cyclase inhibitory pathway / G-protein, beta subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / Adrenaline,noradrenaline inhibits insulin secretion / Thromboxane signalling through TP receptor / G alpha (s) signalling events / Rhodopsin / ADP signalling through P2Y purinoceptor 1 / G alpha (i) signalling events / G alpha (z) signalling events / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (12/13) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / 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 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G beta:gamma signalling through PLC beta / Prostacyclin signalling through prostacyclin receptor / G protein-coupled receptor, rhodopsin-like / G alpha (q) signalling events
Function and homology information
Specimen sourceEscherichia coli (E. coli)
Homo sapiens (human)
Rattus norvegicus (Norway rat)
Bos taurus (cattle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
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.
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
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

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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
Polyers187,3576
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: (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: (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: (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: (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: (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: (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 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 / 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.92 / 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 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 227386 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412812
ELECTRON MICROSCOPYf_angle_d1.00617376
ELECTRON MICROSCOPYf_dihedral_angle_d4.7037623
ELECTRON MICROSCOPYf_chiral_restr0.0591949
ELECTRON MICROSCOPYf_plane_restr0.0072214

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