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 

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This is version 2.0 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: https://doi.org/10.1529/biophysj.107.108225
  • Primary Citation of Related Structures:  
    2PED

  • 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 displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rhodopsin
A, B
349Bos taurusMutation(s): 0 
Gene Names: RHO
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-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
E
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G31886NL
GlyCosmos:  G31886NL
GlyGen:  G31886NL
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HTG
Query on HTG
Download Ideal Coordinates CCD File 
EA [auth B],
FA [auth B],
R [auth A],
S [auth A]		heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N		 Ligand Interaction
RET
Query on RET
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N [auth A],
Z [auth B]		RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N		 Ligand Interaction
PLM
Query on PLM
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AA [auth B]
BA [auth B]
DA [auth B]
O [auth A]
P [auth A]
AA [auth B],
BA [auth B],
DA [auth B],
O [auth A],
P [auth A],
Q [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N		 Ligand Interaction
HG
Query on HG
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G [auth A]
H [auth A]
I [auth A]
T [auth B]
U [auth B]
G [auth A],
H [auth A],
I [auth A],
T [auth B],
U [auth B],
V [auth B]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N		 Ligand Interaction
HTO
Query on HTO
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CA [auth B]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N		 Ligand Interaction
ZN
Query on ZN
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J [auth A]
K [auth A]
L [auth A]
M [auth A]
W [auth B]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
W [auth B],
X [auth B],
Y [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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 = 95.96α = 90
b = 95.96β = 90
c = 150.84γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary