5TE3

Crystal structure of Bos taurus opsin at 2.7 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb5TE3/pdb

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


• Deposited: 2016-09-20 Released: 2017-03-15 
• Deposition Author(s): Gulati, S., Kiser, P.D., Palczewski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.36 kDa 
• Atom Count: 2,792 
• Modelled Residue Count: 326 
• Deposited Residue Count: 348 
• Unique protein chains: 1

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

Oligosaccharides

Help

Entity ID: 2
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	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	C [auth A], D [auth A], I [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	E [auth A], H [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.66	α = 90
b = 242.66	β = 90
c = 111.77	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Gulati, S., Kiser, P.D., Palczewski, K.

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-03-29
  Changes: Database references
• Version 1.2: 2017-04-05
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary