3QAP

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Active State of Sensory Rhodopsin II: Structural Determinants for Signal Transfer and Proton Pumping.

Gushchin, I.Reshetnyak, A.Borshchevskiy, V.Ishchenko, A.Round, E.Grudinin, S.Engelhard, M.Buldt, G.Gordeliy, V.

(2011) J.Mol.Biol. 412: 591-600

  • DOI: 10.1016/j.jmb.2011.07.022
  • Primary Citation of Related Structures:  3QDC

  • PubMed Abstract: 
  • The molecular mechanism of transmembrane signal transduction is still a pertinent question in cellular biology. Generally, a receptor can transfer an external signal via its cytoplasmic surface, as found for G-protein-coupled receptors such as rhodop ...

    The molecular mechanism of transmembrane signal transduction is still a pertinent question in cellular biology. Generally, a receptor can transfer an external signal via its cytoplasmic surface, as found for G-protein-coupled receptors such as rhodopsin, or via the membrane domain, such as that in sensory rhodopsin II (SRII) in complex with its transducer, HtrII. In the absence of HtrII, SRII functions as a proton pump. Here, we report on the crystal structure of the active state of uncomplexed SRII from Natronomonas pharaonis, NpSRII. The problem with a dramatic loss of diffraction quality upon loading of the active state was overcome by growing better crystals and by reducing the occupancy of the state. The conformational changes in the region comprising helices F and G are similar to those observed for the NpSRII-transducer complex but are much more pronounced. The meaning of these differences for the understanding of proton pumping and signal transduction by NpSRII is discussed.


    Organizational Affiliation

    Laboratoire des Protéines Membranaires, Institut de Biologie Structurale J.-P. Ebel, UMR5075 CEA-CNRS-UJF, 38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sensory rhodopsin-2
A
239Natronomonas pharaonisGene Names: sop2 (sopII)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Sensory Rhodopsin II (SRII)
Find proteins for P42196 (Natronomonas pharaonis)
Go to UniProtKB:  P42196
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

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Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
L2P
Query on L2P

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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
LFA
Query on LFA

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Download CCD File 
A
EICOSANE
LIPID FRAGMENT
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

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Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 86.990α = 90.00
b = 128.090β = 90.00
c = 50.630γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-09-28
    Type: Database references