1YCC

HIGH-RESOLUTION REFINEMENT OF YEAST ISO-1-CYTOCHROME C AND COMPARISONS WITH OTHER EUKARYOTIC CYTOCHROMES C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c.

Louie, G.V.Brayer, G.D.

(1990) J.Mol.Biol. 214: 527-555

  • DOI: 10.1016/0022-2836(90)90197-T
  • Also Cited By: 2JQR

  • PubMed Abstract: 
  • The structure of yeast iso-1-cytochrome c has been refined against X-ray diffraction data to a nominal resolution of 1.23 A. The atomic model contains 893 protein atoms, as well as 116 water molecules and one sulfate anion. Also included in the refin ...

    The structure of yeast iso-1-cytochrome c has been refined against X-ray diffraction data to a nominal resolution of 1.23 A. The atomic model contains 893 protein atoms, as well as 116 water molecules and one sulfate anion. Also included in the refinement are 886 hydrogen atoms belonging to the protein molecule. The crystallographic R-factor is 0.192 for the 12,513 reflections with F greater than or equal to 3 sigma (F) in the resolution range 6.0 to 1.23 A. Co-ordinate accuracy is estimated to be better than 0.18 A. The iso-1-cytochrome c molecule has the typical cytochrome c fold, with the polypeptide chain organized into a series of alpha-helices and reverse turns that serve to envelop the heme prosthetic group in a hydrophobic pocket. Inspection of the conformations of helices in the molecule shows that the local environments of the helices, in particular the presence of intrahelical threonine residues, cause distortions from ideal alpha-helical geometry. Analysis of the internal mobility of iso-1-cytochrome c, based on refined crystallographic temperature factors, shows that the most rigid parts of the molecule are those that are closely associated with the heme group. The degree of saturation of hydrogen-bonding potential is high, with 90% of all polar atoms found to participate in hydrogen bonding. The geometry of intramolecular hydrogen bonds is typical of that observed in other high-resolution protein structures. The 116 water molecules present in the model represent about 41% of those expected to be present in the asymmetric unit. The majority of the water molecules are organized into a small number of hydrogen-bonding networks that are anchored to the protein surface. Comparison of the structure of yeast iso-1-cytochrome c with those of tuna and rice cytochromes c shows that these three molecules have very high structural similarity, with the atomic packing in the heme crevice region being particularly highly conserved. Large conformational differences that are observed between these cytochromes c can be explained by amino acid substitutions. Additional subtle differences in the positioning of the side-chains of several highly conserved residues are also observed and occur due to unique features in the local environments of each cytochrome c molecule.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Yeast Iso-1-Cytochrome C. A 2.8 Angstrom Resolution Three-Dimensional Structure Determination.
      Louie, G.V.,Hutcheon, W.L.B.,Brayer, G.D.
      (1988) J.Mol.Biol. 199: 295
    • A Polypeptide Chain-Refolding Event Occurs in the Gly82 Variant of Yeast Iso-1-Cytochrome C
      Louie, G.V.,Brayer, G.D.
      (1989) J.Mol.Biol. 210: 313
    • Role of Phenylalanine-82 in Yeast Iso-1-Cytochrome C and Remote Conformational Changes Induced by a Serine Residue at This Position
      Louie, G.V.,Pielak, G.J.,Smith, M.,Brayer, G.D.
      (1988) Biochemistry 27: 7870


    Organizational Affiliation

    Department of Biochemistry, University of British Columbia, Vancouver, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
A
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.460α = 90.00
b = 36.460β = 90.00
c = 136.860γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-07-15
    Type: Initial release
  • Version 1.1: 2008-03-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other