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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E],
O [auth K],
S [auth O]		98Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P02299 (Drosophila melanogaster)
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Go to UniProtKB:  P02299
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UniProt GroupP02299
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F],
P [auth L],
T [auth P]		79Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P84040 (Drosophila melanogaster)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G],
Q [auth M],
U [auth Q]		102Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P84051 (Drosophila melanogaster)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H],
R [auth N],
V [auth R]		90Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P02283 (Drosophila melanogaster)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CENP-CL [auth U],
K [auth V],
X [auth W],
W [auth X]		25Rattus norvegicusMutation(s): 0 
Gene Names: Cenpc, Cenpc1
UniProt
Find proteins for Q66LH7 (Rattus norvegicus)
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UniProt GroupQ66LH7
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (147-MER)A [auth I],
M [auth S]		147Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (147-MER)B [auth J],
N [auth T]		147Homo sapiens
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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