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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaerhodopsin-2259Halobacterium sp. AUS-2Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P29563 (Halobacterium sp. (strain aus-2))
Explore P29563 
Go to UniProtKB:  P29563
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29563
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L3P
Query on L3P

Download Ideal Coordinates CCD File 
F [auth A]2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
L4P
Query on L4P

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N
22B
Query on 22B

Download Ideal Coordinates CCD File 
C [auth A]BACTERIORUBERIN
C50 H76 O4
UVCQMCCIAHQDAF-CUMPQFAQSA-N
L2P
Query on L2P

Download Ideal Coordinates CCD File 
E [auth A]2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
SQL
Query on SQL

Download Ideal Coordinates CCD File 
I [auth A](6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene
C30 H50
YYGNTYWPHWGJRM-AAJYLUCBSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description