3CYT

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Redox conformation changes in refined tuna cytochrome c.

Takano, T.Dickerson, R.E.

(1980) Proc Natl Acad Sci U S A 77: 6371-6375

  • DOI: 10.1073/pnas.77.11.6371
  • Primary Citation of Related Structures:  
    3CYT

  • PubMed Abstract: 
  • Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78 ...

    Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side.


    Related Citations: 
    • Conformation Change of Cytochrome C. I. Ferrocytochrome C Structure Refined at 1.5 Angstroms Resolution
      Takano, T., Dickerson, R.E.
      (1981) J Mol Biol 153: 79
    • Conformation Change of Cytochrome C. II. Ferricytochrome C Refinement at 1.8 Angstroms and Comparison with the Ferrocytochrome Structure
      Takano, T., Dickerson, R.E.
      (1981) J Mol Biol 153: 95
    • Cytochrome C and the Evolution of Energy Metabolism
      Dickerson, R.E.
      (1980) Sci Am 242: 136
    • Internal Mobility of Ferrocytochrome C
      Northrup, S.H., Pear, M.R., Mccammon, J.A., Karplus, M., Takano, T.
      (1980) Nature 287: 659
    • Tuna Cytochrome C at 2.0 Angstroms Resolution. II. Ferrocytochrome Structure Analysis
      Takano, T., Trus, B.L., Mandel, N., Mandel, G., Kallai, O.B., Swanson, R., Dickerson, R.E.
      (1977) J Biol Chem 252: 776
    • Tuna Cytochrome C at 2.0 Angstroms Resolution. I. Ferricytochrome Structure Analysis
      Swanson, R., Trus, B.L., Mandel, N., Mandel, G., Kallai, O.B., Dickerson, R.E.
      (1977) J Biol Chem 252: 759
    • The Structure of Ferrocytochrome C at 2.45 Angstroms Resolution
      Takano, T., Kallai, O.B., Swanson, R., Dickerson, R.E.
      (1973) J Biol Chem 248: 5234
    • The Structure and History of an Ancient Protein
      Dickerson, R.E.
      (1972) Sci Am 226: 58

    Organizational Affiliation

    the Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME CB [auth I], A [auth O]104Thunnus alalungaMutation(s): 0 
Gene Names: cyc
UniProt
Find proteins for P81459 (Thunnus alalunga)
Explore P81459 
Go to UniProtKB:  P81459
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
C [auth O], D [auth I]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.42α = 90
b = 74.42β = 90
c = 36.3γ = 90

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1980-07-01 
  • Released Date: 1980-09-16 
  • Deposition Author(s): Takano, T.
  • This entry supersedes: 1CYT

Revision History  (Full details and data files)

  • Version 1.0: 1980-09-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary