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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 chain
  • Fab light chain
  • chimera protein of Soluble cytochrome b562 and Rhodopsin
KeywordsSIGNALING PROTEIN / Rhodopsin / G protein / cryo-EM / Structure
Function / homology
Function and homology information


Opsins / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / rod photoreceptor outer segment ...Opsins / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / rod photoreceptor outer segment / cellular response to light stimulus / VxPx cargo-targeting to cilium / thermotaxis / Golgi-associated vesicle membrane / detection of temperature stimulus involved in thermoception / response to light intensity / 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 / photoreceptor cell maintenance / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / 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 / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / ciliary membrane / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / The canonical retinoid cycle in rods (twilight vision) / alkylglycerophosphoethanolamine phosphodiesterase activity / phototransduction, visible light / photoreceptor outer segment / phototransduction / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / photoreceptor inner segment / cardiac muscle cell apoptotic process / sperm midpiece / visual perception / cellular response to forskolin / regulation of mitotic spindle organization / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / G-protein beta/gamma-subunit complex binding / centriolar satellite / microtubule cytoskeleton organization / Activation of the phototransduction cascade / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Rattus norvegicus (Norway rat)
Bos taurus (domestic 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. ...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
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
American Asthma Foundation United States
Jay and Betty Van Andel Foundation United States
Ministry of Science and Technology (MoST, China)2012ZX09301001 and 2012CB910403, 2013CB910600, XDB08020303, 2013ZX09507001 China
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 / ...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
DepositionMar 5, 2018Deposition site: RCSB / Processing site: RCSB
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Revision 1.5Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _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)187,7827
Polymers187,3576
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#2: Protein 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 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 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 (domestic cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212

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Antibody , 2 types, 2 molecules LH

#5: Antibody Fab light chain


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: Antibody Fab Heavy chain


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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Protein / Sugars , 2 types, 2 molecules R

#1: Protein 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
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Details

Has protein modificationY

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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-#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 FIELD
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
EM softwareName: PHENIX / Category: model 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
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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