8PWP | pdb_00008pwp

Light structure of sensory rhodopsin-II solved by serial millisecond crystallography 0-30 milliseconds time-bin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.302 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the prolonged photocycle of sensory rhodopsin II revealed by serial synchrotron crystallography.

Bosman, R.Ortolani, G.Ghosh, S.James, D.Norder, P.Hammarin, G.Ulfarsdottir, T.B.Ostojic, L.Weinert, T.Dworkowski, F.Tomizaki, T.Standfuss, J.Branden, G.Neutze, R.

(2025) Nat Commun 16: 3460-3460

  • DOI: https://doi.org/10.1038/s41467-025-58263-x
  • Primary Citation of Related Structures:  
    8PWG, 8PWI, 8PWJ, 8PWP, 8PWQ, 9H1W, 9H1X, 9H20

  • PubMed Abstract: 

    Microbial rhodopsins form a diverse family of light-sensitive seven-transmembrane helix retinal proteins that function as active proton or ion pumps, passive light-gated ion channels, and photosensors. To understand how light-sensing in archaea is initiated by sensory rhodopsins, we perform serial synchrotron X-ray crystallography (SSX) studies of light induced conformational changes in sensory rhodopsin II (NpSRII) from the archaea Natronomonas pharaonis, both collecting time-resolved SSX data and collecting SSX data during continuous illumination. Comparing light-induced electron density changes in NpSRII with those reported for bacteriorhodopsin (bR) reveals several common light-induced structural perturbations. Unlike bR, however, helix G of NpSRII does not unwind near the conserved lysine residue to which retinal is covalently bound and therefore transient water molecule binding sites do not arise immediately to the cytoplasmic side of retinal. These structural differences prolong the duration of the NpSRII photocycle relative to bR, allowing time for the light-initiated sensory signal to be amplified.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sensory rhodopsin-2249Natronomonas pharaonisMutation(s): 0 
Gene Names: sop2sopII
Membrane Entity: Yes 
UniProt
Find proteins for P42196 (Natronomonas pharaonis)
Explore P42196 
Go to UniProtKB:  P42196
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42196
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.302 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.75α = 90
b = 131.7β = 90
c = 51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union637295

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Database references