2HPY | pdb_00002hpy

Crystallographic model of lumirhodopsin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.238 (Depositor), 0.328 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.343 (DCC) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 

Literature

Local peptide movement in the photoreaction intermediate of rhodopsin

Nakamichi, H., Okada, T.

(2006) Proc Natl Acad Sci U S A 103: 12729-12734

  • DOI: https://doi.org/10.1073/pnas.0601765103
  • Primary Citation Related Structures: 
    2HPY

  • PubMed Abstract: 

    Photoactivation of the visual rhodopsin, a prototypical G protein-coupled receptor (GPCR), involves efficient conversion of the intrinsic inverse-agonist 11-cis-retinal to the all-trans agonist. This event leads to the rearrangement of the heptahelical transmembrane bundle, which is thought to be shared by hundreds of GPCRs. To examine this activation mechanism, we determined the x-ray crystallographic model of the photoreaction intermediate of rhodopsin, lumirhodopsin, which represents the conformational state having the nearly complete all-trans agonist form of the retinal. A difference electron density map clearly indicated that the distorted all-trans-retinal in the precedent intermediate bathorhodopsin relaxes by dislocation of the beta-ionone ring in lumirhodopsin, along with significant peptide displacement in the middle of helix III, including approximately two helical turns. This local movement results in the breaking of the electrostatic interhelical restraints mediated by many of the conserved residues among rhodopsin-like GPCRs, with consequent acquisition of full activity.

    • Organizational Affiliation: 
    • Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.

Macromolecule Content 

  • Total Structure Weight: 85.39 kDa 
  • Atom Count: 5,948 
  • 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

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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: 2.80 Å
  • R-Value Free:  0.238 (Depositor), 0.328 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.343 (DCC) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.72α = 90
b = 96.72β = 90
c = 150.4γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, 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: 2024-10-30
    Changes: Data collection, Database references, Structure summary