3AM6

Crystal structure of the proton pumping rhodopsin AR2 from marine alga Acetabularia acetabulum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.290 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga

Wada, T.Shimono, K.Kikukawa, T.Hato, M.Shinya, N.Kim, S.Y.Kimura-Someya, T.Shirouzu, M.Tamogami, J.Miyauchi, S.Jung, K.-H.Kamo, N.Yokoyama, S.

(2011) J.Mol.Biol. 411: 986-998

  • DOI: 10.1016/j.jmb.2011.06.028

  • PubMed Abstract: 
  • Acetabularia rhodopsin (AR) is a rhodopsin from the marine plant Acetabularia acetabulum. The opsin-encoding gene from A. acetabulum, ARII, was cloned and found to be novel but homologous to that reported previously. ARII is a light-driven proton pum ...

    Acetabularia rhodopsin (AR) is a rhodopsin from the marine plant Acetabularia acetabulum. The opsin-encoding gene from A. acetabulum, ARII, was cloned and found to be novel but homologous to that reported previously. ARII is a light-driven proton pump, as demonstrated by the existence of a photo-induced current through Xenopus oocytes expressing ARII. The photochemical reaction of ARII prepared by cell-free protein synthesis was similar to that of bacteriorhodopsin (BR), except for the lack of light-dark adaptation and the different proton release and uptake sequence. The crystal structure determined at 3.2 Å resolution is the first structure of a eukaryotic member of the microbial rhodopsin family. The structure of ARII is similar to that of BR. From the cytoplasmic side to the extracellular side of the proton transfer pathway in ARII, Asp92, a Schiff base, Asp207, Asp81, Arg78, Glu199, and Ser189 are arranged in positions similar to those of the corresponding residues directly involved in proton transfer by BR. The side-chain carboxyl group of Asp92 appears to interact with the sulfhydryl group of Cys218, which is unique to ARII and corresponds to Leu223 of BR and to Asp217 of Anabaena sensory rhodopsin. The orientation of the Arg78 side chain is opposite to the corresponding Arg82 of BR. The putative absence of water molecules around Glu199 and Arg78 may disrupt the formation of the low-barrier hydrogen bond at Glu199, resulting in the "late proton release".


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
rhodopsin-2
A, B, C, D
229Acetabularia acetabulumMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Acetabularia Rhodopsin II (ARII)
Find proteins for G1K3Q0 (Acetabularia acetabulum)
Go to UniProtKB:  G1K3Q0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A, B, C, D
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A, B, C, D
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.290 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.120α = 90.00
b = 110.487β = 90.00
c = 129.116γ = 90.00
Software Package:
Software NamePurpose
BSSdata collection
REFMACrefinement
CNSrefinement
HKL-2000data reduction
MrBUMPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-08-16 
  • Released Date: 2011-07-06 
  • Deposition Author(s): Wada, T., Yokoyama, S.

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-12-07
    Type: Database references