4J4Q

Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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This is version 2.0 of the entry. See complete history


Literature

Opsin, a structural model for olfactory receptors?

Park, J.H.Morizumi, T.Li, Y.Hong, J.E.Pai, E.F.Hofmann, K.P.Choe, H.W.Ernst, O.P.

(2013) Angew Chem Int Ed Engl 52: 11021-11024

  • DOI: 10.1002/anie.201302374
  • Primary Citation of Related Structures:  
    4J4Q

  • PubMed Abstract: 
  • Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition ...

    Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition.


    Organizational Affiliation

    Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Chonbuk National University, 570-752 Iksan (Republic of Korea). junghee.park@jbnu.ac.kr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhodopsinA348Bos taurusMutation(s): 0 
Gene Names: RHO
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
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Go to UniProtKB:  P02699
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UniProt GroupP02699
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(t) subunit alpha-1B11Bos taurusMutation(s): 2 
Gene Names: GNAT1
Membrane Entity: Yes 
UniProt
Find proteins for P04695 (Bos taurus)
Explore P04695 
Go to UniProtKB:  P04695
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04695
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranoseD 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900006
Query on PRD_900006
DtrehaloseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 241.265α = 90
b = 241.265β = 90
c = 109.561γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary