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- EMDB-4598: Rhodopsin-Gi protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4598
TitleRhodopsin-Gi protein complex
Map data
SampleRhodopsin-Gi complex bound with antibody fragment Fab16
  • (Guanine nucleotide-binding protein ...) x 5
  • antibody FAB fragment Fab16
  • (Rhodopsin) x 2
  • (Fab antibody fragment ...) x 2
  • ligand
Function / homology
Function and homology information


G protein-coupled receptor complex / opsin binding / absorption of visible light / photoreceptor inner segment membrane / 11-cis retinal binding / G protein-coupled photoreceptor activity / cellular response to light stimulus / phototransduction, visible light / G protein-coupled serotonin receptor binding / positive regulation of protein localization to cell cortex ...G protein-coupled receptor complex / opsin binding / absorption of visible light / photoreceptor inner segment membrane / 11-cis retinal binding / G protein-coupled photoreceptor activity / cellular response to light stimulus / phototransduction, visible light / G protein-coupled serotonin receptor binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / arrestin family protein binding / G-protein beta/gamma-subunit complex / cellular response to catecholamine stimulus / photoreceptor cell maintenance / cell cortex region / rhodopsin mediated signaling pathway / outer membrane / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / photoreceptor outer segment membrane / regulation of mitotic spindle organization / photoreceptor disc membrane / cellular response to forskolin / negative regulation of synaptic transmission / G-protein beta/gamma-subunit complex binding / photoreceptor outer segment / heterotrimeric G-protein complex / GTPase activating protein binding / G-protein alpha-subunit binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to light stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cellular response to prostaglandin E stimulus / phototransduction / guanyl-nucleotide exchange factor activity / retina development in camera-type eye / visual perception / response to peptide hormone / G protein-coupled receptor binding / GDP binding / midbody / lysosomal membrane / protein-chromophore linkage / cell-cell junction / protein folding / cell cycle / GTPase activity / cell division / Golgi membrane / centrosome / G protein-coupled receptor signaling pathway / membrane raft / GTP binding / protein phosphorylation / magnesium ion binding / integral component of plasma membrane / zinc ion binding / extracellular exosome / membrane / integral component of membrane / identical protein binding / plasma membrane / nucleus / cytoplasm
G-protein beta WD-40 repeat / G protein alpha subunit, helical insertion / P-loop containing nucleoside triphosphate hydrolase / G protein-coupled receptor, rhodopsin-like / Rhodopsin / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group I / G-protein, beta subunit / Opsin / Visual pigments (opsins) retinal binding site ...G-protein beta WD-40 repeat / G protein alpha subunit, helical insertion / P-loop containing nucleoside triphosphate hydrolase / G protein-coupled receptor, rhodopsin-like / Rhodopsin / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group I / G-protein, beta subunit / Opsin / Visual pigments (opsins) retinal binding site / G-protein, gamma subunit / WD40 repeat / G-protein gamma-like domain / WD40 repeat, conserved site / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Guanine nucleotide-binding protein, beta subunit / GPCR, rhodopsin-like, 7TM / WD40-repeat-containing domain / Rhodopsin, N-terminal / G-protein gamma-like domain superfamily
Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Rhodopsin / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Biological speciesHomo sapiens (human) / Bos taurus (cattle) / Mus musculus (house mouse) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.38 Å
AuthorsTsai C-J / Marino J / Adaixo RJ / Pamula F / Muehle J / Maeda S / Flock T / Taylor NMI / Mohammed I / Matile H / Dawson RJP / Deupi X / Stahlberg H / Schertler GFX
Funding support Switzerland, 5 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_153145 Switzerland
Swiss National Science Foundation160805 Switzerland
Swiss National Science Foundation310030B_173335 Switzerland
Swiss National Science FoundationNCCR TransCure Switzerland
Swiss Nanoscience InstituteA13.12 NanoGhip Switzerland
CitationJournal: Elife / Year: 2019
Title: Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit.
Authors: Ching-Ju Tsai / Jacopo Marino / Ricardo Adaixo / Filip Pamula / Jonas Muehle / Shoji Maeda / Tilman Flock / Nicholas Mi Taylor / Inayatulla Mohammed / Hugues Matile / Roger Jp Dawson / ...Authors: Ching-Ju Tsai / Jacopo Marino / Ricardo Adaixo / Filip Pamula / Jonas Muehle / Shoji Maeda / Tilman Flock / Nicholas Mi Taylor / Inayatulla Mohammed / Hugues Matile / Roger Jp Dawson / Xavier Deupi / Henning Stahlberg / Gebhard Schertler /
Abstract: One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently ...One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently heterotrimeric G proteins. The recent surge in structural data has expanded our understanding of GPCR-mediated signal transduction. However, many aspects, including the existence of transient interactions, remain elusive. We present the cryo-EM structure of the light-sensitive GPCR rhodopsin in complex with heterotrimeric Gi. Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. By comparing available complexes, we found a small set of common anchoring points that are G protein-subtype specific. Taken together, our structure and analysis provide new structural basis for the molecular events of the GPCR signaling pathway.
Validation ReportPDB-ID: 6qno

SummaryFull reportAbout validation report
History
DepositionFeb 11, 2019-
Header (metadata) releaseMar 6, 2019-
Map releaseJul 10, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qno
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4598.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 338 pix.
= 280.54 Å
0.83 Å/pix.
x 338 pix.
= 280.54 Å
0.83 Å/pix.
x 338 pix.
= 280.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.050998867 - 0.12045996
Average (Standard dev.)0.00039033938 (±0.0034118635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions338338338
Spacing338338338
CellA=B=C: 280.54 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z338338338
origin x/y/z0.0000.0000.000
length x/y/z280.540280.540280.540
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS338338338
D min/max/mean-0.0510.1200.000

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Supplemental data

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Sample components

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Entire Rhodopsin-Gi complex bound with antibody fragment Fab16

EntireName: Rhodopsin-Gi complex bound with antibody fragment Fab16
Number of components: 12

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Component #1: protein, Rhodopsin-Gi complex bound with antibody fragment Fab16

ProteinName: Rhodopsin-Gi complex bound with antibody fragment Fab16
Recombinant expression: No
MassExperimental: 170 kDa

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Component #2: protein, Guanine nucleotide-binding protein alpha subunit

ProteinName: Guanine nucleotide-binding protein alpha subunit / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #3: protein, Guanine nucleotide-binding protein beta/gamma subunit

ProteinName: Guanine nucleotide-binding protein beta/gamma subunit / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Component #4: protein, antibody FAB fragment Fab16

ProteinName: antibody FAB fragment Fab16 / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: hybrid (others)

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Component #5: protein, Rhodopsin

ProteinName: Rhodopsin / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: 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: 43.182078 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #7: 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: 37.41693 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #8: protein, Guanine nucleotide-binding protein G(T) subunit gamma-T1

ProteinName: Guanine nucleotide-binding protein G(T) subunit gamma-T1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.556918 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #9: protein, Fab antibody fragment light chain

ProteinName: Fab antibody fragment light chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.309551 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: hybrid (others)

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Component #10: protein, Fab antibody fragment heavy chain

ProteinName: Fab antibody fragment heavy chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.558902 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: hybrid (others)

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Component #11: protein, Rhodopsin

ProteinName: Rhodopsin / Details: mutant N2C/M257Y/D282C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.040527 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human)
Source (natural)Organ or tissue: retina

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Component #12: ligand, RETINAL

LigandName: RETINAL / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.284436 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL
Buffer solution: The detergent lauryl-maltose neopentyl glycol (LMNG) was used before the last purification step by gel filtration. In the gel filtration, detergent-free buffer was used.
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 90 %

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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: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 165000 X (nominal), 165000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 15000.0 - 25000.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (70.0 - 93.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3200 / Sampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 115000 / Details: super resolution mode
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 6FUF, 1GOT, 6QNK
Output model

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