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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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: 

    Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhodopsinA316Bos taurusMutation(s): 3 
Gene Names: RHO
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alphaB214Homo sapiensMutation(s): 8 
Gene Names: GNAO1
Find proteins for P09471 (Homo sapiens)
Explore P09471 
Go to UniProtKB:  P09471
NIH Common Fund Data Resources
PHAROS  P09471
GTEx  ENSG00000087258
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET
Download Ideal Coordinates CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
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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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 

  • 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