3QAP

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  
    3QAP, 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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sensory rhodopsin-2A239Natronomonas pharaonisMutation(s): 0 
Gene Names: sop2, sopII
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Bacterial, Algal, and viral Rhodopsins		Protein: 
Sensory Rhodopsin II (SRII) in active state
Find proteins for P42196 (Natronomonas pharaonis)
Explore P42196 
Go to UniProtKB:  P42196
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L2P
Query on L2P
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A
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N		 Ligand Interaction
BOG
Query on BOG
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A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
RET
Query on RET
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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N		 Ligand Interaction
LFA
Query on LFA
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A
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.99α = 90
b = 128.09β = 90
c = 50.63γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary