5MJC

metNeuroglobin under oxygen at 50 bar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments.

Ardiccioni, C.Arcovito, A.Della Longa, S.van der Linden, P.Bourgeois, D.Weik, M.Montemiglio, L.C.Savino, C.Avella, G.Exertier, C.Carpentier, P.Prange, T.Brunori, M.Colloc'h, N.Vallone, B.

(2019) Iucrj 6: 832-842

  • DOI: 10.1107/S2052252519008157
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in g ...

    A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo , solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O 2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.


    Related Citations: 
    • Neuroglobin, nitric oxide, and oxygen: functional pathways and conformational changes.
      Brunori, M.,Giuffre, A.,Nienhaus, K.,Nienhaus, G.U.,Scandurra, F.M.,Vallone, B.
      (2005) Proc. Natl. Acad. Sci. U.S.A. 102: 8483


    Organizational Affiliation

    Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy.,Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.,Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy.,ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France.,Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France.,Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences 'A. Rossi Fanelli', University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.,CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France.,Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy.,Department of Biochemical Sciences 'A. Rossi Fanelli', University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.,Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France.,Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy.,European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France.,CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France.,Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy.




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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
DIO
Query on DIO

Download SDF File 
Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 87.351α = 90.00
b = 87.351β = 90.00
c = 112.650γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references
  • Version 1.2: 2019-07-10
    Type: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2019-10-16
    Type: Data collection, Database references