Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24065.20 
• Atom Count: 1692 
• Residue Count: 208 
• Unique protein chains: 1

3CYT

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

• DOI: 10.2210/pdb3CYT/pdb
• Entry 3CYT supersedes 1CYT

• Classification: ELECTRON TRANSPORT (HEME PROTEIN)
• Organism(s): Thunnus alalunga


• Deposited: 1980-07-01 Released: 1980-09-16 
• Deposition Author(s): Takano, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å

Literature

Redox conformation changes in refined tuna cytochrome c.

Takano, T., Dickerson, R.E.

(1980) Proc.Natl.Acad.Sci.USA 77: 6371-6375

• PubMed: 6256733 
• DOI: 10.1073/pnas.77.11.6371


• 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. 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.

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Related Citations: 

• The Structure and History of an Ancient Protein
  Dickerson, R.E.
  (1972) Sci.Am. 226: 58
• 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
• 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
• Internal Mobility of Ferrocytochrome C
  Northrup, S.H.,Pear, M.R.,Mccammon, J.A.,Karplus, M.,Takano, T.
  (1980) Nature 287: 659
• 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
• 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
• Cytochrome C and the Evolution of Energy Metabolism
  Dickerson, R.E.
  (1980) Sci.Am. 242: 136
• 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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYTOCHROME C	O, I	104	Thunnus alalunga	Mutation(s): 0  Gene Names: cyc
Find proteins for P81459 (Thunnus alalunga) Go to UniProtKB:  P81459

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	I, O	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	I, O	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• Space Group: P 4₃

Unit Cell:

Length (Å)	Angle (°)
a = 74.420	α = 90.00
b = 74.420	β = 90.00
c = 36.300	γ = 90.00

Structure Validation

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 

• Version 1.0: 1980-09-16
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-11-29
  Type: Derived calculations, Other