5NW6

Crystal structure of murine neuroglobin under 50 bar krypton pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 

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
  • Primary Citation of Related Structures:  

  • 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.


    Organizational Affiliation

    ISTCT CNRS UNICAEN CEA Normandie University, CERVOxy Team, Centre Cyceron, Caen, France. Electronic address: colloch@cyceron.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuroglobin
A
148Mus musculusMutation(s): 2 
Gene Names: Ngb
Find proteins for Q9ER97 (Mus musculus)
Go to UniProtKB:  Q9ER97
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 89.126α = 90.00
b = 89.126β = 90.00
c = 115.265γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references
  • Version 1.2: 2018-02-21
    Type: Structure summary