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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A
348Bos taurusGene Names: RHO
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Rhodopsin
Find proteins for P02699 (Bos taurus)
Go to Gene View: RHO
Go to UniProtKB:  P02699
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(t) subunit alpha-1
B
11Bos taurusGene Names: GNAT1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Rhodopsin
Find proteins for P04695 (Bos taurus)
Go to Gene View: GNAT1
Go to UniProtKB:  P04695
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRE
Query on TRE

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Download CCD File 
A
TREHALOSE
ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE
C12 H22 O11
HDTRYLNUVZCQOY-LIZSDCNHSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

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Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 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 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 241.265α = 90.00
b = 241.265β = 90.00
c = 109.561γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release