1UFI | pdb_00001ufi

Crystal structure of the dimerization domain of human CENP-B

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.309 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

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This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution

Tawaramoto, M.S., Park, S.-Y., Tanaka, Y., Nureki, O., Kurumizaka, H., Yokoyama, S.

(2003) J Biological Chem 278: 51454-51461

  • DOI: https://doi.org/10.1074/jbc.M310388200
  • Primary Citation Related Structures: 
    1UFI

  • PubMed Abstract: 

    The human centromere protein B (CENP-B), a centromeric heterochromatin component, forms a homodimer that specifically binds to a distinct DNA sequence (the CENP-B box), which appears within every other alpha-satellite repeat. Previously, we determined the structure of the human CENP-B DNA-binding domain, CENP-B-(1-129), complexed with the CENP-B box DNA. In the present study, we determined the crystal structure of its dimerization domain (CENP-B-(540-599)), another functional domain of CENP-B, at 1.65-A resolution. CENP-B-(540-599) contains two alpha-helices, which are folded into an antiparallel configuration. The CENP-B-(540-599) dimer formed a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. In the CENP-B-(540-599) dimer, the N-terminal ends of CENP-B-(540-599) are oriented on opposite sides of the dimer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation.

    • Organizational Affiliation: 
    • RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Macromolecule Content 

  • Total Structure Weight: 29 kDa 
  • Atom Count: 1,694 
  • Modeled Residue Count: 188 
  • Deposited Residue Count: 256 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major centromere autoantigen B
A, B, C, D
64Homo sapiensMutation(s): 0 
Gene Names: CENPB
UniProt & NIH Common Fund Data Resources
Find proteins for P07199 (Homo sapiens)
Explore P07199 
Go to UniProtKB:  P07199
PHAROS:  P07199
GTEx:  ENSG00000125817 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07199
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.309 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.707α = 90
b = 48.955β = 90
c = 100.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references