4J4Q

Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside

• PDB DOI: https://doi.org/10.2210/pdb4J4Q/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2013-02-07 Released: 2013-10-30 
• Deposition Author(s): Park, J.H., Morizumi, T., Li, Y., Hong, J.E., Pai, E.F., Hofmann, K.P., Choe, H.W., Ernst, O.P.

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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 

Starting Model: experimental

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

• PubMed: 24038729 
• DOI: https://doi.org/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.

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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). [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.06 kDa 
• Atom Count: 2,920 
• Modelled Residue Count: 337 
• Deposited Residue Count: 359 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	348	Bos taurus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(t) subunit alpha-1	B	11	Bos taurus	Mutation(s): 2  Membrane Entity: Yes
UniProt
Find proteins for P04695 (Bos taurus) Explore P04695  Go to UniProtKB:  P04695

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	E [auth A], F [auth A], G [auth A], H [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	I [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
SO4	J [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	K [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	D	trehalose	Oligosaccharide / Nutrient

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 = 241.265	α = 90
b = 241.265	β = 90
c = 109.561	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Park, J.H., Morizumi, T., Li, Y., Hong, J.E., Pai, E.F., Hofmann, K.P., Choe, H.W., Ernst, O.P.

Revision History  

• 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
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary