5DYS

Crystal Structure of T94I rhodopsin mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural role of the T94I rhodopsin mutation in congenital stationary night blindness.

Singhal, A.Guo, Y.Matkovic, M.Schertler, G.Deupi, X.Yan, E.C.Standfuss, J.

(2016) Embo Rep. 17: 1431-1440

  • DOI: 10.15252/embr.201642671
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Congenital stationary night blindness (CSNB) is an inherited and non-progressive retinal dysfunction. Here, we present the crystal structure of CSNB-causing T94I <sup>2.61 </sup> rhodopsin in the active conformation at 2.3 Å resolution. The introduce ...

    Congenital stationary night blindness (CSNB) is an inherited and non-progressive retinal dysfunction. Here, we present the crystal structure of CSNB-causing T94I 2.61 rhodopsin in the active conformation at 2.3 Å resolution. The introduced hydrophobic side chain prolongs the lifetime of the G protein activating metarhodopsin-II state by establishing a direct van der Waals contact with K296 7.43 , the site of retinal attachment. This is in stark contrast to the light-activated state of the CSNB-causing G90D 2.57 mutation, where the charged mutation forms a salt bridge with K296 7.43 To find the common denominator between these two functional modifications, we combined our structural data with a kinetic biochemical analysis and molecular dynamics simulations. Our results indicate that both the charged G90D 2.57 and the hydrophobic T94I 2.61 mutation alter the dark state by weakening the interaction between the Schiff base (SB) and its counterion E113 3.28 We propose that this interference with the tight regulation of the dim light photoreceptor rhodopsin increases background noise in the visual system and causes the loss of night vision characteristic for CSNB patients.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT, USA.,Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland.,Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland joerg.standfuss@psi.ch.,Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland Deparment of Biology, ETH Zurich, Zürich, Switzerland.,Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A
349Bos taurusMutation(s): 3 
Gene Names: RHO
Find proteins for P02699 (Bos taurus)
Go to Gene View: RHO
Go to UniProtKB:  P02699
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
RET
Query on RET

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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

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A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.219 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 242.301α = 90.00
b = 242.301β = 90.00
c = 112.055γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Switzerland--

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references