6FUF

Crystal structure of the rhodopsin-mini-Go complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of rhodopsin in complex with a mini-Gosheds light on the principles of G protein selectivity.

Tsai, C.J.Pamula, F.Nehme, R.Muhle, J.Weinert, T.Flock, T.Nogly, P.Edwards, P.C.Carpenter, B.Gruhl, T.Ma, P.Deupi, X.Standfuss, J.Tate, C.G.Schertler, G.F.X.

(2018) Sci Adv 4: eaat7052-eaat7052

  • DOI: https://doi.org/10.1126/sciadv.aat7052
  • Primary Citation of Related Structures:  
    6FUF

  • PubMed Abstract: 

    Selective coupling of G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-G o protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a "structural switch," allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR-G protein interface suggests that the precise position of the carboxyl-terminal "hook-like" element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.


  • Organizational Affiliation

    Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin316Bos taurusMutation(s): 3 
Gene Names: RHO
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alpha214Homo sapiensMutation(s): 8 
Gene Names: GNAO1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens)
Explore P09471 
Go to UniProtKB:  P09471
PHAROS:  P09471
GTEx:  ENSG00000087258 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09471
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.359α = 90
b = 151.359β = 90
c = 96.652γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_153145
Swiss National Science FoundationSwitzerland310030B_173335
Swiss National Science FoundationSwitzerland310030B_173335
Swiss National Science FoundationSwitzerland31003A_159558
European Research CouncilUnited KingdomEMPSI, 339995

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary