2PED

Crystallographic model of 9-cis-rhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography

Nakamichi, H.Buss, V.Okada, T.

(2007) Biophys.J. 92: L106-L108

  • DOI: 10.1529/biophysj.107.108225

  • PubMed Abstract: 
  • The primary photochemical process of the visual function has been investigated using the three crystallographic models, 11-cis-rhodopsin, all-trans-bathorhodopsin, and the artificial isomeric 9-cis-rhodopsin. Detailed examination of the atomic displa ...

    The primary photochemical process of the visual function has been investigated using the three crystallographic models, 11-cis-rhodopsin, all-trans-bathorhodopsin, and the artificial isomeric 9-cis-rhodopsin. Detailed examination of the atomic displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency.


    Related Citations: 
    • Protein assistance in the photoisomerization of rhodopsin and 9-cis-rhodopsin--insights from experiment and theory
      Sekharan, S.,Sugihara, M.,Weingart, O.,Okada, T.,Buss, V.
      (2007) J.Am.Chem.Soc. 129: 1052


    Organizational Affiliation

    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A, B
349Bos taurusGene Names: RHO
Find proteins for P02699 (Bos taurus)
Go to Gene View: RHO
Go to UniProtKB:  P02699
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HTG
Query on HTG

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A, B
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 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, B
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
BMA
Query on BMA

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B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
HTO
Query on HTO

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B
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
NAG
Query on NAG

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

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A, B
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

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A, B
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 95.960α = 90.00
b = 95.960β = 90.00
c = 150.840γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance