6EYE

Crystal structure of murine neuroglobin under 150 bar krypton


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure.

Colloc'h, N.Carpentier, P.Montemiglio, L.C.Vallone, B.Prange, T.

(2017) Biophys J 113: 2199-2206

  • DOI: 10.1016/j.bpj.2017.10.014
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein l ...

    Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.


    Related Citations: 
    • Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia
      Abraini, J.H., Marassio, G., David, H.N., Vallone, B., Prange, T., Colloc'h, N.
      (2014) Anesthesiology 121: 1018
    • Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel "soak-and-freeze" methodology
      Lafumat, B., Mueller-Dieckmann, C., Gordon, L., Colloc'h, N., Prange, T., Giraud, T., Dobias, F., Royant, A., van der Linden, P., Carpentier, P.
      (2016) J Of Applied Crystallogr 49: 1478

    Organizational Affiliation

    LCRB, UMR 8015 CNRS Université Paris Descartes, Paris, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NeuroglobinA154Mus musculusMutation(s): 2 
Gene Names: Ngb
Find proteins for Q9ER97 (Mus musculus)
Explore Q9ER97 
Go to UniProtKB:  Q9ER97
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
KR
Query on KR

Download CCD File 
A
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.854α = 90
b = 87.854β = 90
c = 113.21γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references, Structure summary
  • Version 1.2: 2019-09-04
    Changes: Data collection, Structure summary