Structure of Human NADH cytochrome b5 oxidoreductase (Ncb5or) b5 Domain to 1.25A Resolution

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 

Starting Model: experimental
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Study of the individual cytochrome b5 and cytochrome b5 reductase domains of Ncb5or reveals a unique heme pocket and a possible role of the CS domain.

Deng, B.Parthasarathy, S.Wang, W.Gibney, B.R.Battaile, K.P.Lovell, S.Benson, D.R.Zhu, H.

(2010) J Biol Chem 285: 30181-30191

  • DOI: https://doi.org/10.1074/jbc.M110.120329
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NADH cytochrome b(5) oxidoreductase (Ncb5or) is found in animals and contains three domains similar to cytochrome b(5) (b(5)), CHORD-SGT1 (CS), and cytochrome b(5) reductase (b(5)R). Ncb5or has an important function, as suggested by the diabetes and lipoatrophy phenotypes in Ncb5or null mice. To elucidate the structural and functional properties of human Ncb5or, we generated its individual b(5) and b(5)R domains (Ncb5or-b(5) and Ncb5or-b(5)R, respectively) and compared them with human microsomal b(5) (Cyb5A) and b(5)R (Cyb5R3). A 1.25 Å x-ray crystal structure of Ncb5or-b(5) reveals nearly orthogonal planes of the imidazolyl rings of heme-ligating residues His(89) and His(112), consistent with a highly anisotropic low spin EPR spectrum. Ncb5or is the first member of the cytochrome b(5) family shown to have such a heme environment. Like other b(5) family members, Ncb5or-b(5) has two helix-loop-helix motifs surrounding heme. However, Ncb5or-b(5) differs from Cyb5A with respect to location of the second heme ligand (His(112)) and of polypeptide conformation in its vicinity. Electron transfer from Ncb5or-b(5)R to Ncb5or-b(5) is much less efficient than from Cyb5R3 to Cyb5A, possibly as a consequence of weaker electrostatic interactions. The CS linkage probably obviates the need for strong interactions between b(5) and b(5)R domains in Ncb5or. Studies with a construct combining the Ncb5or CS and b(5)R domains suggest that the CS domain facilitates docking of the b(5) and b(5)R domains. Trp(114) is an invariant surface residue in all known Ncb5or orthologs but appears not to contribute to electron transfer from the b(5)R domain to the b(5) domain.

  • Organizational Affiliation

    Department of Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, Kansas 66160, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b5 reductase 4
A, B
88Homo sapiensMutation(s): 0 
Gene Names: CYB5R4NCB5OR
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L1T6 (Homo sapiens)
Explore Q7L1T6 
Go to UniProtKB:  Q7L1T6
GTEx:  ENSG00000065615 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L1T6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.48α = 90
b = 56.37β = 100.67
c = 42.56γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-03-29
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description