4HYJ

Crystal structure of Exiguobacterium sibiricum rhodopsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria.

Gushchin, I.Chervakov, P.Kuzmichev, P.Popov, A.N.Round, E.Borshchevskiy, V.Ishchenko, A.Petrovskaya, L.Chupin, V.Dolgikh, D.A.Arseniev, A.A.Kirpichnikov, M.Gordeliy, V.

(2013) Proc.Natl.Acad.Sci.USA 110: 12631-12636

  • DOI: 10.1073/pnas.1221629110

  • PubMed Abstract: 
  • Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR po ...

    Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features. First, ESR's proton donor is a lysine side chain that is situated very close to the bulk solvent. Second, the α-helical structure in the middle of the helix F is replaced by 3(10)- and π-helix-like elements that are stabilized by the Trp-154 and Asn-224 side chains. This feature is characteristic for the proteorhodopsin family of proteins. Third, the proton release region is connected to the bulk solvent by a chain of water molecules already in the ground state. Despite these peculiarities, the positions of water molecule and amino acid side chains in the immediate Schiff base vicinity are very well conserved. These features make ESR a very unusual proton pump. The presented structure sheds light on the large family of proteorhodopsins, for which structural information was not available previously.


    Organizational Affiliation

    Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, 38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A, B
258Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15)Mutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, and viral Rhodopsins
Protein: 
Proteorhodopsin
Find proteins for B1YFV8 (Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15))
Go to UniProtKB:  B1YFV8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

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

Download SDF File 
Download CCD File 
A, B
EICOSANE
LIPID FRAGMENT
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.099α = 90.00
b = 96.099β = 90.00
c = 124.380γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references