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- EMDB-7517: Rhodopsin-Gi -

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Entry
Database: EMDB / ID: 7517
TitleRhodopsin-Gi
Map dataprimary map
SampleProtein complex of Rhodopsin with Galphai
  • chimera protein of Soluble cytochrome b562 and Rhodopsin
  • (Guanine nucleotide-binding protein ...) x 3
  • Fab light chainFragment antigen-binding
  • Fab Heavy chainFragment antigen-binding
  • ligand
Function / homologyGPCR, rhodopsin-like, 7TM / 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. ...GPCR, rhodopsin-like, 7TM / 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. / 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 / G beta:gamma signalling through PI3Kgamma / G-protein alpha subunit / 7 transmembrane receptor (rhodopsin family) / Adrenaline,noradrenaline inhibits insulin secretion / Guanine nucleotide-binding protein, beta subunit / Opsin / G-protein, gamma subunit / Cytochrome b562 / Cytochrome c/b562 / G protein alpha subunit, helical insertion / G-protein gamma-like domain / WD40/YVTN repeat-like-containing domain superfamily / Ca2+ pathway / WD40-repeat-containing domain superfamily / 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 / Prostacyclin signalling through prostacyclin receptor / Ca2+ pathway / G-protein, beta subunit / 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) / G alpha (q) signalling events / Thromboxane signalling through TP receptor / 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 / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G-protein activation / 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 / PLC beta mediated events / Adenylate cyclase inhibitory pathway / WD40 repeat / G-protein alpha subunit, group I / Adrenaline,noradrenaline inhibits insulin secretion / Thromboxane signalling through TP receptor / G alpha (s) signalling events / Guanine nucleotide binding protein (G-protein), alpha subunit / 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 alpha (q) signalling events
Function and homology information
SourceHomo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (cattle) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsKang Y / Kuybeda O / de Waal PW / Mukherjee S / Van Eps N / Dutka P / Zhou XE / Bartesaghi A / Erramilli S / Morizumi T / Gu X / Yin Y / Liu P / Jiang Y / Meng X / Zhao G / Melcher K / Earnst OP / Kossiakoff AA / Subramaniam S / Xu HE
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 ReportPDB-ID: 6cmo

SummaryFull reportAbout validation report
DateDeposition: Mar 5, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Jun 20, 2018 / Last update: Feb 20, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cmo
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7517.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.09 Å/pix.
= 278.528 Å
256 pix
1.09 Å/pix.
= 278.528 Å
256 pix
1.09 Å/pix.
= 278.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density
Contour Level:0.063 (by emdb), 0.045 (movie #1):
Minimum - Maximum-0.12783152 - 0.20725927
Average (Standard dev.)0.00056864065 (0.0054518194)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 278.528 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z278.528278.528278.528
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1280.2070.001

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Supplemental data

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Sample components

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Entire Protein complex of Rhodopsin with Galphai

EntireName: Protein complex of Rhodopsin with Galphai / Number of components: 8

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Component #1: protein, Protein complex of Rhodopsin with Galphai

ProteinName: Protein complex of Rhodopsin with Galphai / Recombinant expression: No
MassExperimental: 180 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, chimera protein of Soluble cytochrome b562 and Rhodopsin

ProteinName: chimera protein of Soluble cytochrome b562 and Rhodopsin
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.385406 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Guanine nucleotide-binding protein G(i) subunit alpha-1

ProteinName: Guanine nucleotide-binding protein G(i) subunit alpha-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.445059 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #4: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.915496 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.56375 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: protein, Fab light chain

ProteinName: Fab light chainFragment antigen-binding / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.258783 kDa
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Bacteria Latreille et al. 1825 (Bacteria stick insect)

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Component #7: protein, Fab Heavy chain

ProteinName: Fab Heavy chainFragment antigen-binding / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.788822 kDa
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Bacteria Latreille et al. 1825 (Bacteria stick insect)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 9 mg/ml / pH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.92 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 227386
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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