4X23

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 

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:  4INM

  • 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). W ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E, K, O
98Drosophila melanogasterGene Names: His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Find proteins for P02299 (Drosophila melanogaster)
Go to UniProtKB:  P02299
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L, P
79Drosophila melanogasterGene Names: His4, His4r, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909 (H4, H4r)
Find proteins for P84040 (Drosophila melanogaster)
Go to UniProtKB:  P84040
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G, M, Q
102Drosophila melanogasterGene Names: His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865 (H2a)
Find proteins for P84051 (Drosophila melanogaster)
Go to UniProtKB:  P84051
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H, N, R
90Drosophila melanogasterGene Names: His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Find proteins for P02283 (Drosophila melanogaster)
Go to UniProtKB:  P02283
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
CENP-C
V, U, X, W
25Rattus norvegicusGene Names: Cenpc (Cenpc1)
Find proteins for Q66LH7 (Rattus norvegicus)
Go to UniProtKB:  Q66LH7
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (147-MER)I,S147Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (147-MER)J,T147Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 102.994α = 90.00
b = 176.102β = 90.00
c = 208.846γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CBASSdata collection
SCALEPACKdata scaling
PHASERphasing
XDSdata reduction
CNSrefinement
PHENIXrefinement
Blu-Icedata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Derived calculations
  • Version 1.2: 2016-07-13
    Type: Derived calculations
  • Version 1.3: 2017-11-22
    Type: Advisory, Derived calculations, Refinement description