Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40599.25 
• Atom Count: 2691 
• Residue Count: 349 
• Unique protein chains: 1

4BEZ

Night blindness causing G90D rhodopsin in the active conformation

• DOI: 10.2210/pdb4BEZ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bos taurus
• Expression System: Homo sapiens
• Mutation(s): 3 


• Deposited: 2013-03-12 Released: 2013-04-24 
• Deposition Author(s): Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A., Panneels, V., Homan, K.T., Tesmer, J.J.G., Veprintsev, D., Deupi, X., Gurevich, V.V., Schertler, G.F.X., Standfuss, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.3 Å
• R-Value Free: 0.244 
• R-Value Work: 0.229 

Literature

Insights Into Congenital Stationary Night Blindness Based on the Structure of G90D Rhodopsin.

Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A., Panneels, V., Homan, K.T., Tesmer, J.J., Veprintsev, D., Deupi, X., Gurevich, V.V., Schertler, G.F., Standfuss, J.

(2013) Embo Rep. 14: 520

• PubMed: 23579341 
• DOI: 10.1038/embor.2013.44
• Primary Citation of Related Structures:  
  4BEY


• PubMed Abstract: 
  

We present active-state structures of the G protein-coupled receptor (GPCRs) rhodopsin carrying the disease-causing mutation G90D. Mutations of G90 cause either retinitis pigmentosa (RP) or congenital stationary night blindness (CSNB), a milder, non-progressive form of RP. Our analysis shows that the CSNB-causing G90D mutation introduces a salt bridge with K296. The mutant thus interferes with the E113Q-K296 activation switch and the covalent binding of the inverse agonist 11-cis-retinal, two interactions that are crucial for the deactivation of rhodopsin. Other mutations, including G90V causing RP, cannot promote similar interactions. We discuss our findings in context of a model in which CSNB is caused by constitutive activation of the visual signalling cascade.

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Organizational Affiliation: 

Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen 5232, Switzerland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RHODOPSIN	A	349	Bos taurus	Mutation(s): 3  Gene Names: RHO
Find proteins for P02699 (Bos taurus) Go to Gene View: RHO Go to UniProtKB:  P02699

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.3 Å
• R-Value Free: 0.244 
• R-Value Work: 0.229 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 242.440	α = 90.00
b = 242.440	β = 90.00
c = 110.360	γ = 120.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-12 
• Released Date: 2013-04-24 
• Deposition Author(s): Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A., Panneels, V., Homan, K.T., Tesmer, J.J.G., Veprintsev, D., Deupi, X., Gurevich, V.V., Schertler, G.F.X., Standfuss, J.

Revision History 

• Version 1.0: 2013-04-24
  Type: Initial release
• Version 1.1: 2013-06-19
  Type: Database references