2PED | pdb_00002ped

Crystallographic model of 9-cis-rhodopsin

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 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 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.

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

Macromolecule Content 

  • Total Structure Weight: 85.39 kDa 
  • Atom Count: 5,990 
  • Modeled Residue Count: 698 
  • Deposited Residue Count: 698 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rhodopsin
A, B
349Bos taurusMutation(s): 0 
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: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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
Glycosylation Resources
GlyTouCan: G62182OO
GlyCosmos: G62182OO
GlyGen: G62182OO
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD 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
Glycosylation Resources
GlyTouCan: G31886NL
GlyCosmos: G31886NL
GlyGen: G31886NL

Small Molecules

Ligands 6 Unique
IDChains Name / 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
RET

Query on RET


Download:Ideal Coordinates CCD File
N [auth A],
Z [auth B]		RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
PLM

Query on PLM


Download:Ideal Coordinates CCD File
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
HG

Query on HG


Download:Ideal Coordinates CCD File
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
HTO

Query on HTO


Download:Ideal Coordinates CCD File
CA [auth B]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.289 (Depositor) 
  • R-Value Work:  0.243 (Depositor) 
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
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary