4X23

CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C.

Kato, H., Jiang, J.S., Zhou, B.R., Rozendaal, M., Feng, H., Ghirlando, R., Xiao, T.S., Straight, A.F., Bai, Y.

(2013) Science 340: 1110-1113

  • DOI: https://doi.org/10.1126/science.1235532
  • Primary Citation of Related Structures:  
    4X23

  • PubMed Abstract: 

    Chromosome segregation during mitosis requires assembly of the kinetochore complex at the centromere. Kinetochore assembly depends on specific recognition of the histone variant CENP-A in the centromeric nucleosome by centromere protein C (CENP-C). We have defined the determinants of this recognition mechanism and discovered that CENP-C binds a hydrophobic region in the CENP-A tail and docks onto the acidic patch of histone H2A and H2B. We further found that the more broadly conserved CENP-C motif uses the same mechanism for CENP-A nucleosome recognition. Our findings reveal a conserved mechanism for protein recruitment to centromeres and a histone recognition mode whereby a disordered peptide binds the histone tail through hydrophobic interactions facilitated by nucleosome docking.

    • Organizational Affiliation: 

    Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA.


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E],
O [auth K],
S [auth O]		98Drosophila melanogasterMutation(s): 0 
Gene Names: His3
UniProt
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02299
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F],
P [auth L],
T [auth P]		79Drosophila melanogasterMutation(s): 0 
Gene Names: His4
UniProt
Find proteins for P84040 (Drosophila melanogaster)
Explore P84040 
Go to UniProtKB:  P84040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84040
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G],
Q [auth M],
U [auth Q]		102Drosophila melanogasterMutation(s): 0 
Gene Names: His2A
UniProt
Find proteins for P84051 (Drosophila melanogaster)
Explore P84051 
Go to UniProtKB:  P84051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84051
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H],
R [auth N],
V [auth R]		90Drosophila melanogasterMutation(s): 0 
Gene Names: His2B
UniProt
Find proteins for P02283 (Drosophila melanogaster)
Explore P02283 
Go to UniProtKB:  P02283
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02283
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CENP-CK [auth V],
L [auth U],
W [auth X],
X [auth W]		25Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q66LH7 (Rattus norvegicus)
Explore Q66LH7 
Go to UniProtKB:  Q66LH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ66LH7
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (147-MER)A [auth I],
M [auth S]		147Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (147-MER)B [auth J],
N [auth T]		147Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.994α = 90
b = 176.102β = 90
c = 208.846γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Blu-Icedata collection
CBASSdata collection
HKL-2000data scaling
CNSrefinement
PHASERphasing
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2014-12-10 
    • Deposition Author(s): Jiang, J.S.
  • This entry supersedes: 4INM

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Derived calculations
  • Version 1.2: 2016-07-13
    Changes: Derived calculations
  • Version 1.3: 2017-11-22
    Changes: Advisory, Derived calculations, Refinement description
  • Version 1.4: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description