1B5A

RAT FERROCYTOCHROME B5 A CONFORMATION, NMR, 1 STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: CLOSEST TO THE AVERAGE STRUCTURE, LOW TARGET FUNCTION 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The origin of differences in the physical properties of the equilibrium forms of cytochrome b5 revealed through high-resolution NMR structures and backbone dynamic analyses.

Dangi, B.Sarma, S.Yan, C.Banville, D.L.Guiles, R.D.

(1998) Biochemistry 37: 8289-8302

  • DOI: 10.1021/bi9801964
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • On the basis of a comparison of high-resolution solution structures calculated for both equilibrium forms of rat ferrocytochrome b5, differences in reduction potential and thermodyanmic stability have been characterized in terms of significant struct ...

    On the basis of a comparison of high-resolution solution structures calculated for both equilibrium forms of rat ferrocytochrome b5, differences in reduction potential and thermodyanmic stability have been characterized in terms of significant structural and dynamic differences between the two forms. The dominant difference between A and B conformations has long been known to be due to a 180 degrees rotation of the heme in the binding pocket about an axis defined by the alpha- and gamma-meso carbons, however, the B form has not been structurally characterized until now. The most significant differences observed between the two forms were the presence of a hydrogen bond between the 7-propionate and the S64 amide in the A form but not the B form and surprisingly a displacement of the heme out of the binding pocket by 0.9 A in the B form relative to the A form. The magnitude of other factors which could contribute to the known difference in reduction potentials in the bovine protein [Walker, F. A., Emrick, D., Rivera, J. E., Hanquet, B. J., and Buttlaire, D. H. (1988) J. Am. Chem. Soc. 110, 6234-6240], such as differences in the orientation of the axial imidazoles and differences in hydrogen bond strength to the imidazoles, have been evaluated. The dominant effector of the reduction potential would appear to be the lack of the hydrogen bond to the S64 amide in the B form which frees up the propionate to charge stabilize the iron in the oxidized state and thus lower the reduction potential of the B form. The structure we report for the A form, based on heteronuclear NMR restraints, involving a total of 1288 restraints strongly resembles both the X-ray crystal structure of the bovine protein and a recently reported structure for the A form of the rat protein based on homonuclear data alone [Banci, L., Bertini, I., Ferroni, F., and Rosato, A. (1997) Eur. J. Biochem. 249, 270-279]. The rmsd for the backbone atoms of the A form is 0.54 A (0.92 A for all non-hydrogens). The rmsd for the backbone of the B form is 0.51 A (0. 90 A for all non-hydrogen atoms). An analysis of backbone dynamics based on a model-free analysis of 15N relaxation data, which incorporated axially symmetric diffusion tensor modeling of the cytochrome, indicates that the protein is more rigid in the reduced state relative to the oxidized state, based on a comparison with order parameters reported for the bovine protein in the oxidized state [Kelly, G. P., Muskett, F. W., and Whitford, D. (1997) Eur. J. Biochem. 245, 349-354].


    Organizational Affiliation

    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERROCYTOCHROME B5
A
94Rattus norvegicusMutation(s): 0 
Gene Names: Cyb5a (Cyb5)
Find proteins for P00173 (Rattus norvegicus)
Go to UniProtKB:  P00173
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: CLOSEST TO THE AVERAGE STRUCTURE, LOW TARGET FUNCTION 
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other
  • Version 1.4: 2018-08-08
    Type: Data collection, Experimental preparation, Source and taxonomy