4BEZ | pdb_00004bez

Night blindness causing G90D rhodopsin in the active conformation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.244 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1038/embor.2013.44
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 40.55 kDa 
  • Atom Count: 2,703 
  • Modeled Residue Count: 327 
  • Deposited Residue Count: 349 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RHODOPSIN349Bos taurusMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.244 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.44α = 90
b = 242.44β = 90
c = 110.36γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary