Structure of Human Type B Cytochrome b5

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

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Accommodating a Non-Conservative Internal Mutation by Water-Mediated Hydrogen-Bonding Between beta-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b5

Parthasarathy, S.Altuve, A.Terzyan, S.Zhang, X.Kuczera, K.Rivera, M.Benson, D.R.

(2011) Biochemistry 50: 5544-5554

  • DOI: https://doi.org/10.1021/bi2004729
  • Primary Citation of Related Structures:  
    3MUS, 3NER

  • PubMed Abstract: 

    Mammalian type B (mitochondrial) b(5) cytochromes exhibit greater amino acid sequence diversity than their type A (microsomal) counterparts, as exemplified by the type B proteins from human (hCYB5B) and rat (rCYB5B). The comparison of X-ray crystal structures of hCYB5B and rCYB5B reported herein reveals a striking difference in packing involving the five-strand β-sheet, which can be attributed to fully buried residue 21 in strand β4. The greater bulk of Leu21 in hCYB5B in comparison to that of Thr21 in rCYB5B results in a substantial displacement of the first two residues in β5, and consequent loss of two of the three hydrogen bonds between β5 and β4. Hydrogen bonding between the residues is instead mediated by two well-ordered, fully buried water molecules. In a 10 ns molecular dynamics simulation, one of the buried water molecules in the hCYB5B structure exchanged readily with solvent via intermediates having three water molecules sandwiched between β4 and β5. When the buried water molecules were removed prior to a second 10 ns simulation, β4 and β5 formed persistent hydrogen bonds identical to those in rCYB5B, but the Leu21 side chain was forced to adopt a rarely observed conformation. Despite the apparently greater ease of access of water to the interior of hCYB5B than of rCYB5B suggested by these observations, the two proteins exhibit virtually identical stability, dynamic, and redox properties. The results provide new insight into the factors stabilizing the cytochrome b(5) fold.

  • Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b5 type B
A, B
92Homo sapiensMutation(s): 0 
Gene Names: CYB5BCYB5MOMB5
UniProt & NIH Common Fund Data Resources
Find proteins for O43169 (Homo sapiens)
Explore O43169 
Go to UniProtKB:  O43169
PHAROS:  O43169
GTEx:  ENSG00000103018 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43169
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.316α = 90
b = 40.034β = 98.61
c = 58.744γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description