5F0B

Crystal structure of murine neuroglobin mutant F106W at 280 MPa pressure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography.

Colloc'h, N.Sacquin-Mora, S.Avella, G.Dhaussy, A.C.Prange, T.Vallone, B.Girard, E.

(2017) Sci Rep 7: 1858-1858

  • DOI: 10.1038/s41598-017-02097-1
  • Primary Citation of Related Structures:  
    5EV5, 5EYS, 5EYJ, 5EET, 5EOH, 5F0B, 5EQM, 5F2A, 5EU2

  • PubMed Abstract: 
  • Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to ...

    Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the "heme sliding mechanism". Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.


    Organizational Affiliation

    Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France. eric.girard@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuroglobinA149Mus musculusMutation(s): 3 
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 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.212α = 90
b = 86.212β = 90
c = 114.459γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references