Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 122.58 kDa 
• Atom Count: 8635 
• Modelled Residue Count: 1027 
• Deposited Residue Count: 1066 
• Unique protein chains: 1

3FSN

Crystal structure of RPE65 at 2.14 angstrom resolution

• PDB DOI: 10.2210/pdb3FSN/pdb

• Classification: ISOMERASE
• Organism(s): Bos taurus
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2009-01-11 Released: 2009-09-29 
• Deposition Author(s): Kiser, P.D., Lodowski, D.T., Palczewski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.216 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Crystal structure of native RPE65, the retinoid isomerase of the visual cycle.

Kiser, P.D., Golczak, M., Lodowski, D.T., Chance, M.R., Palczewski, K.

(2009) Proc Natl Acad Sci U S A 106: 17325-17330

• PubMed: 19805034 
• DOI: 10.1073/pnas.0906600106
• Primary Citation of Related Structures:  
  3FSN


• PubMed Abstract: 
  

Vertebrate vision is maintained by the retinoid (visual) cycle, a complex enzymatic pathway that operates in the retina to regenerate the visual chromophore, 11-cis-retinal. A key enzyme in this pathway is the microsomal membrane protein RPE65. This enzyme catalyzes the conversion of all-trans-retinyl esters to 11-cis-retinol in the retinal pigment epithelium (RPE). Mutations in RPE65 are known to be responsible for a subset of cases of the most common form of childhood blindness, Leber congenital amaurosis (LCA). Although retinoid isomerase activity has been attributed to RPE65, its catalytic mechanism remains a matter of debate. Also, the manner in which RPE65 binds to membranes and extracts retinoid substrates is unclear. To gain insight into these questions, we determined the crystal structure of native bovine RPE65 at 2.14-A resolution. The structural, biophysical, and biochemical data presented here provide the framework needed for an in-depth understanding of the mechanism of catalytic isomerization and membrane association, in addition to the role mutations that cause LCA have in disrupting protein function.

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Organizational Affiliation: 

Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal pigment epithelium-specific 65 kDa protein	A, B	533	Bos taurus	Mutation(s): 1  Gene Names: RPE65 EC: 5.2.1.7 (PDB Primary Data), 3.1.1.64 (UniProt), 5.3.3.22 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q28175 (Bos taurus) Explore Q28175  Go to UniProtKB:  Q28175

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A], F [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
FE2	C [auth A], E [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.216 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.516	α = 90
b = 176.516	β = 90
c = 86.862	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-11 
• Released Date: 2009-09-29 
Deposition Author(s): Kiser, P.D., Lodowski, D.T., Palczewski, K.

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary