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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3C [auth A], G [auth E], O [auth K], S [auth O]98Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B], H [auth F], P [auth L], T [auth P]79Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84040 (Drosophila melanogaster)
Explore P84040 
Go to UniProtKB:  P84040
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C], I [auth G], Q [auth M], U [auth Q]102Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84051 (Drosophila melanogaster)
Explore P84051 
Go to UniProtKB:  P84051
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BF [auth D], J [auth H], R [auth N], V [auth R]90Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02283 (Drosophila melanogaster)
Explore P02283 
Go to UniProtKB:  P02283
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CENP-CL [auth U], K [auth V], X [auth W], W [auth X]25Rattus norvegicusMutation(s): 0 
Gene Names: CenpcCenpc1
Find proteins for Q66LH7 (Rattus norvegicus)
Explore Q66LH7 
Go to UniProtKB:  Q66LH7
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (147-MER)A [auth I], M [auth S]147Homo sapiens
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (147-MER)B [auth J], N [auth T]147Homo sapiens
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



Entry History 

Deposition Data

  • Deposited Date: 2014-11-25 
  • 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