4J4Q | pdb_00004j4q

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 PDBTM MemProtMD mpstruc

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.230 (Depositor), 0.227 (DCC)
R-Value Work:
0.217 (Depositor), 0.215 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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

PubMed: 24038729 Search on PubMed
DOI: https://doi.org/10.1002/anie.201302374
Primary Citation 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.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02699
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04695
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B]	J [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	D	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.230 (Depositor), 0.227 (DCC)
R-Value Work: 0.217 (Depositor), 0.215 (DCC)
R-Value Observed: 0.218 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

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