5AX0

Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.52 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.521 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum

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

(2015) Acta Crystallogr.,Sect.D 71: 2203-2216

  • DOI: 10.1107/S1399004715015722
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine ...

    Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52-1.80 Å) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pKa of Glu206(ARI), which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97(ARI) and Tyr221(ARI) on the cytoplasmic side, which facilitates the slow photocycle and regulates the pKa of Asp100(ARI), a potential proton donor to the Schiff base, in the dark state.


    Organizational Affiliation

    Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 121-742, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin I
A
244Acetabularia acetabulumMutation(s): 0 
Gene Names: aopI
Find proteins for G3CEP6 (Acetabularia acetabulum)
Go to UniProtKB:  G3CEP6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R16
Query on R16

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A
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
 Ligand Interaction
OLB
Query on OLB

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A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
D12
Query on D12

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A
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
C14
Query on C14

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A
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
RET
Query on RET

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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
D10
Query on D10

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A
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.521 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.990α = 90.00
b = 101.630β = 119.17
c = 43.760γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references