1L9H

Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.

Okada, T.Fujiyoshi, Y.Silow, M.Navarro, J.Landau, E.M.Shichida, Y.

(2002) Proc Natl Acad Sci U S A 99: 5982-5987

  • DOI: 10.1073/pnas.082666399
  • Primary Citation of Related Structures:  
    1L9H

  • PubMed Abstract: 
  • Activation of G protein-coupled receptors (GPCRs) is triggered and regulated by structural rearrangement of the transmembrane heptahelical bundle containing a number of highly conserved residues. In rhodopsin, a prototypical GPCR, the helical bundle accommodates an intrinsic inverse-agonist 11-cis-retinal, which undergoes photo-isomerization to the all-trans form upon light absorption ...

    Activation of G protein-coupled receptors (GPCRs) is triggered and regulated by structural rearrangement of the transmembrane heptahelical bundle containing a number of highly conserved residues. In rhodopsin, a prototypical GPCR, the helical bundle accommodates an intrinsic inverse-agonist 11-cis-retinal, which undergoes photo-isomerization to the all-trans form upon light absorption. Such a trigger by the chromophore corresponds to binding of a diffusible ligand to other GPCRs. Here we have explored the functional role of water molecules in the transmembrane region of bovine rhodopsin by using x-ray diffraction to 2.6 A. The structural model suggests that water molecules, which were observed in the vicinity of highly conserved residues and in the retinal pocket, regulate the activity of rhodopsin-like GPCRs and spectral tuning in visual pigments, respectively. To confirm the physiological relevance of the structural findings, we conducted single-crystal microspectrophotometry on rhodopsin packed in our three-dimensional crystals and show that its spectroscopic properties are similar to those previously found by using bovine rhodopsin in suspension or membrane environment.


    Organizational Affiliation

    Department of Biophysics, Graduate School of Science, Kyoto University, and Core Research for Evolution Science and Technology (CREST), Japan Science and Technology Corporation, Kyoto 606-8502, Japan. okada@photo2.biophys.kyoto-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
rhodopsinA, B349Bos taurusMutation(s): 0 
Gene Names: RHO
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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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-glucopyranoseC3N-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-glucopyranoseD, F2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G48068RF
GlyCosmos:  G48068RF
GlyGen:  G48068RF
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNG (Subject of Investigation/LOI)
Query on BNG

Download Ideal Coordinates CCD File 
AA [auth B], BA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
JA [auth B], X [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
IA [auth B], KA [auth B], W [auth A], Y [auth A], Z [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download Ideal Coordinates CCD File 
CA [auth B], DA [auth B], EA [auth B], L [auth A], M [auth A], N [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

Download Ideal Coordinates CCD File 
S [auth A], T [auth A], U [auth A], V [auth A]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth B], GA [auth B], HA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.745α = 90
b = 96.745β = 90
c = 149.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 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