6CMO

Rhodopsin-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Cryo-EM structure of human rhodopsin bound to an inhibitory G protein.

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.Ernst, O.P.Kossiakoff, A.A.Subramaniam, S.Xu, H.E.

(2018) Nature 558: 553-558

  • DOI: 10.1038/s41586-018-0215-y

  • PubMed 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 hetrotrimeric G proteins G <sub>s </sub> (stimulat ...

    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 s (stimulatory) and G i (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 i are mediated by the C-terminal helix of the G i 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 i -bound and arrestin-bound forms of rhodopsin with inactive and G s -bound forms of the β 2 -adrenergic receptor provide a foundation to understand the unique structural signatures that are associated with the recognition of G s , G i and arrestin by activated G-protein-coupled receptors.


    Organizational Affiliation

    Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. eric.xu@vai.org.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. ss1@nih.gov.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. koss@bsd.uchicago.edu.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. ss1@nih.gov.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. koss@bsd.uchicago.edu.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA. eric.xu@vai.org.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
chimera protein of Soluble cytochrome b562 and Rhodopsin
R
463Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 0 
Gene Names: RHO (OPN2), cybC
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Human rhodopsin with bound mouse visual arrestin
Find proteins for P08100 (Homo sapiens)
Go to Gene View: RHO
Go to UniProtKB:  P08100
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1
A
354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Human rhodopsin with bound mouse visual arrestin
Find proteins for P63096 (Homo sapiens)
Go to Gene View: GNAI1
Go to UniProtKB:  P63096
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
345Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Human rhodopsin with bound mouse visual arrestin
Find proteins for P54311 (Rattus norvegicus)
Go to UniProtKB:  P54311
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G
68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Human rhodopsin with bound mouse visual arrestin
Find proteins for P63212 (Bos taurus)
Go to Gene View: GNG2
Go to UniProtKB:  P63212
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Fab Heavy chain
H
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
R
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK071662
American Asthma FoundationUnited States--
Jay and Betty Van Andel FoundationUnited States--
Ministry of Science and Technology (China)China2012ZX09301001 and 2012CB910403, 2013CB910600, XDB08020303, 2013ZX09507001

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references, Structure summary
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-04-17
    Type: Author supporting evidence, Data collection