Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17347.42 
• Atom Count: 1269 
• Residue Count: 148 
• Unique protein chains: 1

5EET

Crystal structure of murine neuroglobin at ambient pressure

• DOI: 10.2210/pdb5EET/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• Deposited: 2015-10-23 Released: 2016-10-19 
• Deposition Author(s): Colloc'h, N., Girard, E., Vallone, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.180 
• R-Value Work: 0.143 

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

• PubMed: 28500341 
• DOI: 10.1038/s41598-017-02097-1
• Primary Citation of Related Structures:  
  5F2A, 5F0B, 5EYS, 5EYJ, 5EV5, 5EU2, 5EQM, 5EOH


• 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 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.

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Organizational Affiliation: 

ISTCT CNRS UNICAEN CEA Normandie Univ., CERVOxy team, centre Cyceron, 14000, Caen, France. [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Neuroglobin	A	148	Mus musculus	Mutation(s): 2  Gene Names: Ngb
Find proteins for Q9ER97 (Mus musculus) Go to UniProtKB:  Q9ER97

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.180 
• R-Value Work: 0.143 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 88.316	α = 90.00
b = 88.316	β = 90.00
c = 114.457	γ = 120.00

Software Package:

Software Name	Purpose
SCALA	data scaling
SCALA	data scaling
PHASER	phasing
PHASER	phasing
DM	phasing
BUCCANEER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-23 
• Released Date: 2016-10-19 
• Deposition Author(s): Colloc'h, N., Girard, E., Vallone, B.

Revision History 

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