3WQJ

Crystal structure of archaerhodopsin-2 at 1.8 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of archaerhodopsin-2 at 1.8 angstrom resolution.

Kouyama, T., Fujii, R., Kanada, S., Nakanishi, T., Chan, S.K., Murakami, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2692-2701

  • DOI: 10.1107/S1399004714017313
  • Primary Citation of Related Structures:  
    3WQJ

  • PubMed Abstract: 

    • Archaerhodopsin-2 (aR2), the sole protein found in the claret membrane of Halorubrum sp. Aus-2, functions as a light-driven proton pump. In this study, structural analysis of aR2 was performed using a novel three-dimensional crystal prepared by the successive fusion of claret membranes ...

    Archaerhodopsin-2 (aR2), the sole protein found in the claret membrane of Halorubrum sp. Aus-2, functions as a light-driven proton pump. In this study, structural analysis of aR2 was performed using a novel three-dimensional crystal prepared by the successive fusion of claret membranes. The crystal is made up of stacked membranes, in each of which aR2 trimers are arranged on a hexagonal lattice. This lattice structure resembles that found in the purple membrane of H. salinarum, except that lipid molecules trapped within the trimeric structure are not distributed with perfect threefold symmetry. Nonetheless, diffraction data at 1.8 Å resolution provide accurate structural information about functionally important residues. It is shown that two glutamates in the proton-release channel form a paired structure that is maintained by a low-barrier hydrogen bond. Although the structure of the proton-release pathway is highly conserved among proton-pumping archaeal rhodopsins, aR2 possesses the following peculiar structural features: (i) the motional freedom of the tryptophan residue that makes contact with the C13 methyl group of retinal is restricted, affecting the formation/decay kinetics of the L state, and (ii) the N-terminal polypeptide folds into an Ω-loop, which may play a role in organizing the higher-order structure.

    Organizational Affiliation: 

    Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Archaerhodopsin-2 A259Halobacterium sp. AUS-2Mutation(s): 0 
Find proteins for P29563 (Halobacterium sp. (strain aus-2))
Explore P29563 
Go to UniProtKB:  P29563
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L3P
Query on L3P
Download Ideal Coordinates CCD File 
A
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L		 Ligand Interaction
L4P
Query on L4P
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A
3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N		 Ligand Interaction
22B
Query on 22B
Download Ideal Coordinates CCD File 
A
BACTERIORUBERIN
C50 H76 O4
UVCQMCCIAHQDAF-CUMPQFAQSA-N		 Ligand Interaction
L2P
Query on L2P
Download Ideal Coordinates CCD File 
A
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N		 Ligand Interaction
SQL
Query on SQL
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A
(6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene
C30 H50
YYGNTYWPHWGJRM-AAJYLUCBSA-N		 Ligand Interaction
RET
Query on RET
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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N		 Ligand Interaction
SO4
Query on SO4
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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.739α = 90
b = 62.739β = 90
c = 331.464γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-01-27 
  • Released Date: 2014-10-15 
    • Deposition Author(s): Kouyama, T.

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references, Derived calculations