3CAP

Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State

• PDB DOI: https://doi.org/10.2210/pdb3CAP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2008-02-20 Released: 2008-06-24 
• Deposition Author(s): Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 82.68 kDa 
• Atom Count: 5,504 
• Modelled Residue Count: 652 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-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, E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGL	G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B]	2-O-octyl-beta-D-glucopyranose C14 H28 O6 BVHPDIWLWHHJPD-RKQHYHRCSA-N
PLM	K [auth A], N [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.917	α = 90
b = 242.918	β = 90
c = 110.42	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary