2EI4

Trimeric complex of archaerhodopsin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2

Yoshimura, K.Kouyama, T.

(2008) J.Mol.Biol. 375: 1267-1281

  • DOI: 10.1016/j.jmb.2007.11.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Archaerhodopsin-2 (aR2), a retinal protein-carotenoid complex found in the claret membrane of Halorubrum sp. aus-2, functions as a light-driven proton pump. In this study, the membrane fusion method was utilized to prepare trigonal P321 crystals (a=b ...

    Archaerhodopsin-2 (aR2), a retinal protein-carotenoid complex found in the claret membrane of Halorubrum sp. aus-2, functions as a light-driven proton pump. In this study, the membrane fusion method was utilized to prepare trigonal P321 crystals (a=b=98.2 A, c=56.2 A) and hexagonal P6(3) crystals (a=b=108.8 A, c=220.7 A). The trigonal crystal is made up of stacked membranes in which the aR2 trimers are arranged on a honeycomb lattice. Similar membranous structures are found in the hexagonal crystal, but four membrane layers with different orientations are contained in the unit cell. In these crystals, the carotenoid bacterioruberin [5,32-bis(2-hydroxypropan-2-yl)-2,8,12,16,21,25,29,35-octamethylhexatriaconta-6,8,10,12,14,16,18,20,22,24,26,28,30-tridecaene-2,35-diol] binds to crevices between the subunits of the trimer. Its polyene chain is inclined from the membrane normal by an angle of about 20 degrees and, on the cytoplasmic side, it is surrounded by helices AB and DE of neighbouring subunits. This peculiar binding mode suggests that bacterioruberin plays a striking structural role for the trimerization of aR2. When compared with the aR2 structure in another crystal form containing no bacterioruberin, the proton release channel takes a more closed conformation in the P321 or P6(3) crystal; i.e., the native conformation of protein is stabilized in the trimeric protein-bacterioruberin complex. Interestingly, most residues participating in the trimerization are not conserved in bacteriorhodopsin, a homologous protein capable of forming a trimeric structure in the absence of bacterioruberin. Despite a large alteration in the amino acid sequence, the shape of the intratrimer hydrophobic space filled by lipids is highly conserved between aR2 and bacteriorhodopsin. Since a transmembrane helix facing this space undergoes a large conformational change during the proton pumping cycle, it is feasible that trimerization is an important strategy to capture special lipid components that are relevant to the protein activity.


    Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Archaerhodopsin-2
A
253Halobacterium sp. (strain aus-2)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Archaerhodopsin-2 (aR-2)
Find proteins for P29563 (Halobacterium sp. (strain aus-2))
Go to UniProtKB:  P29563
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
22B
Query on 22B

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Download CCD File 
A
BACTERIORUBERIN
C50 H76 O4
UVCQMCCIAHQDAF-CUMPQFAQSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
L2P
Query on L2P

Download SDF File 
Download CCD File 
A
2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.188 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.160α = 90.00
b = 98.160β = 90.00
c = 56.160γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97phasing
SHELXL-97model building
SHELXL-97refinement
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-03-11 
  • Released Date: 2008-01-01 
  • Deposition Author(s): Kouyama, T.

Revision History 

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance