3ARL

Cl- binding hemoglobin component V form Propsilocerus akamusi under 500 mM NaCl at pH 5.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Involvement of the distal Arg residue in Cl- binding of midge larval haemoglobin

Kuwada, T.Hasegawa, T.Takagi, T.Sakae, T.Sato, I.Shishikura, F.

(2011) Acta Crystallogr D Biol Crystallogr 67: 488-495

  • DOI: https://doi.org/10.1107/S0907444911010808
  • Primary Citation of Related Structures:  
    3ARJ, 3ARK, 3ARL

  • PubMed Abstract: 

    Monomeric haemoglobin component V (Hb V) from the larva of the midge Propsilocerus akamusi shows high Cl⁻ affinity under high salt concentrations at acidic pH. In order to understand the structural changes that depend on Cl⁻ binding, crystal structures of Hb V were determined under acidic high-salt conditions and the structural changes arising from different haem-bound ligands were simulated. Crystal structures of Hb V under acidic high-salt conditions indicated that the side chain of ArgE10 on the distal face of the haem contributes to stabilizing haem-bound Cl⁻. The conformation of the Arg side chain in the Cl⁻-bound form was almost identical to that in ligated Hb V at neutral pH but not to that in met Hb V under acidic salt-free conditions. Furthermore, preliminary molecular-dynamics simulations also indicated that the swinging of the Arg side chain into the haem pocket depends on Cl⁻ ligation. This result suggests that, like pH change, Cl⁻ binding affects the location of the distal Arg residue. Owing to the increased positive electrostatic potential observed in the haem pocket at acidic pH, it was concluded that electrostatic changes caused by pH change and anionic ligand binding may affect the behaviour of the polar Arg residue.


  • Organizational Affiliation

    Laboratory for Electron Beam Research and Application (LEBRA), Institute of Quantum Science, Nihon University, Funabashi, Chiba 274-8501, Japan. kuwadat@lebra.nihon-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin V152Tokunagayusurika akamusiMutation(s): 0 
UniProt
Find proteins for Q7M422 (Tokunagayusurika akamusi)
Explore Q7M422 
Go to UniProtKB:  Q7M422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M422
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.33α = 90
b = 75.15β = 90
c = 33.47γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description