Skip to main content

 6CMO | pdb_00006cmo

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

Validation slider image for 6CMO

This is version 2.2 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: https://doi.org/10.1038/s41586-018-0215-y
  • Primary Citation 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. 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: 
    • Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.

Macromolecule Content 

  • Total Structure Weight: 187.78 kDa 
  • Atom Count: 11,834 
  • Modeled Residue Count: 1,516 
  • Deposited Residue Count: 1,684 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
chimera protein of Soluble cytochrome b562 and RhodopsinA [auth R]463Escherichia coli, Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybC, RHO, OPN2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08100 (Homo sapiens)
Explore P08100 
Go to UniProtKB:  P08100
PHAROS:  P08100
GTEx:  ENSG00000163914 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP08100P0ABE7
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P08100-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63096
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]345Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54311
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63212
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab light chainE [auth L]215synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab Heavy chainF [auth H]239synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 2.2: 2025-05-28
    Changes: Data collection