Biological Assembly 1  

 3D View: Structure | 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: 40.55 kDa 
• Atom Count: 2703 
• Modelled Residue Count: 327 
• Deposited 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): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.244 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

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, 4BEZ


• 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.

---

Organizational Affiliation: 

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

Macromolecules

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG (Subject of Investigation/LOI)	F [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM (Subject of Investigation/LOI)	E [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.244 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.44	α = 90
b = 242.44	β = 90
c = 110.36	γ = 120

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary