3CYT | pdb_00003cyt

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

• PDB DOI: https://doi.org/10.2210/pdb3CYT/pdb
• Entry: 3CYT supersedes: 1CYT

• Classification: ELECTRON TRANSPORT (HEME PROTEIN)
• Organism(s): Thunnus alalunga
• Mutation(s): No 


• 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: 1.80 Å

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

• PubMed: 6256733 
• DOI: https://doi.org/10.1073/pnas.77.11.6371
• Primary Citation 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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.07 kDa 
• Atom Count: 1,743 
• Modeled Residue Count: 208 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C	A [auth O], B [auth I]	104	Thunnus alalunga	Mutation(s): 0
UniProt
Find proteins for P81459 (Thunnus alalunga) Explore P81459  Go to UniProtKB:  P81459

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth O], D [auth I]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.42	α = 90
b = 74.42	β = 90
c = 36.3	γ = 90

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary