6CMO

Rhodopsin-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    6CMO

  • 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 s (stimulatory) and G i (inhibitory) and several arrestin proteins ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
chimera protein of Soluble cytochrome b562 and RhodopsinA [auth R]463Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCRHOOPN2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
Human rhodopsin with bound inhibitory G protein (Gi)
Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
Find proteins for P08100 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P08100
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
Human rhodopsin with bound inhibitory G protein (Gi)
Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]345Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
Find proteins for P54311 (Rattus norvegicus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors: Class A
Protein: 
Human rhodopsin with bound inhibitory G protein (Gi)
Find proteins for P63212 (Bos taurus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chainE [auth L]215synthetic constructMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Fab Heavy chainF [auth H]239synthetic constructMutation(s): 0 
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Oligosaccharides

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Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary