4GYC

Structure of the SRII(D75N mutant)/HtrII Complex in I212121 space group ("U" shape)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


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Literature

Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer.

Ishchenko, A.Round, E.Borshchevskiy, V.Grudinin, S.Gushchin, I.Klare, J.P.Balandin, T.Remeeva, A.Engelhard, M.Buldt, G.Gordeliy, V.

(2013) J Photochem Photobiol B 123C: 55-58

  • DOI: https://doi.org/10.1016/j.jphotobiol.2013.03.008
  • Primary Citation of Related Structures:  
    4GYC

  • PubMed Abstract: 

    The complex of sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII) mediates negative phototaxis in halobacteria Natronomonas pharaonis. Upon light activation NpSRII triggers, by means of NpHtrII, a signal transduction chain homologous to the two component system in eubacterial chemotaxis. Here we report on the crystal structure of the ground state of the mutant NpSRII-D75N/NpHtrII complex in the space group I212121. Mutations of this aspartic acid in light-driven proton pumps dramatically modify or/and inhibit protein functions. However, in vivo studies show that the similar D75N mutation retains functionality of the NpSRII/NpHtrII complex. The structure provides the molecular basis for the explanation of the unexpected observation that the wild and the mutant complexes display identical physiological response on light excitation.


  • Organizational Affiliation

    Institute of Complex Systems (ICS), ICS-5: Molecular Biophysics, Research Centre Juelich, 52425 Juelich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sensory rhodopsin-2245Natronomonas pharaonisMutation(s): 1 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sensory rhodopsin II transducer135Natronomonas pharaonisMutation(s): 0 
Gene Names: htr2htrII
Membrane Entity: Yes 
UniProt
Find proteins for P42259 (Natronomonas pharaonis)
Explore P42259 
Go to UniProtKB:  P42259
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42259
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

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

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.465α = 90
b = 113.674β = 90
c = 126.185γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Structure summary
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description