4MPM

Wild-type human neuroglobin

• PDB DOI: https://doi.org/10.2210/pdb4MPM/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-13 Released: 2014-01-15 
• Deposition Author(s): Guimaraes, B.G., Golinelli-Pimpaneau, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

The crystal structure of wild-type human brain neuroglobin reveals flexibility of the disulfide bond that regulates oxygen affinity.

Guimaraes, B.G., Hamdane, D., Lechauve, C., Marden, M.C., Golinelli-Pimpaneau, B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1005-1014

• PubMed: 24699645 
• DOI: https://doi.org/10.1107/S1399004714000078
• Primary Citation of Related Structures:  
  4MPM


• PubMed Abstract: 
  

  Neuroglobin plays an important function in the supply of oxygen in nervous tissues. In human neuroglobin, a cysteine at position 46 in the loop connecting the C and D helices of the globin fold is presumed to form an intramolecular disulfide bond with Cys55. Rupture of this disulfide bridge stabilizes bi-histidyl haem hexacoordination, causing an overall decrease in the affinity for oxygen. Here, the first X-ray structure of wild-type human neuroglobin is reported at 1.74 Å resolution. This structure provides a direct observation of two distinct conformations of the CD region containing the intramolecular disulfide link and highlights internal cavities that could be involved in ligand migration and/or are necessary to enable the conformational transition between the low and high oxygen-affinity states following S-S bond formation.

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Organizational Affiliation: 

Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91190 Gif-sur-Yvette, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 35.14 kDa 
• Atom Count: 2,663 
• Modelled Residue Count: 295 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroglobin	A, B	151	Homo sapiens	Mutation(s): 0  Gene Names: NGB EC: 1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPG2 (Homo sapiens) Explore Q9NPG2  Go to UniProtKB:  Q9NPG2
PHAROS:  Q9NPG2 GTEx:  ENSG00000165553

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.15	α = 90
b = 48.49	β = 90
c = 39.28	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Guimaraes, B.G., Golinelli-Pimpaneau, B.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description