1HLV | pdb_00001hlv

CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA

• PDB DOI: https://doi.org/10.2210/pdb1HLV/pdb
• NAKB: 1HLV

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-12-04 Released: 2002-01-11 
• Deposition Author(s): Tanaka, Y., Nureki, O., Kurumizaka, H., Fukai, S., Kawaguchi, S., Ikuta, M., Iwahara, J., Okazaki, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.222 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.

Tanaka, Y., Nureki, O., Kurumizaka, H., Fukai, S., Kawaguchi, S., Ikuta, M., Iwahara, J., Okazaki, T., Yokoyama, S.

(2001) EMBO J 20: 6612-6618

• PubMed: 11726497 
• DOI: https://doi.org/10.1093/emboj/20.23.6612
• Primary Citation Related Structures: 
  1HLV


• PubMed Abstract: 
  

  The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every other alpha-satellite repeat. In the present study, the crystal structure of the complex of the DNA-binding region (129 residues) of CENP-B and the CENP-B box DNA has been determined at 2.5 A resolution. The DNA-binding region forms two helix-turn-helix domains, which are bound to adjacent major grooves of the DNA. The DNA is kinked at the two recognition helix contact sites, and the DNA region between the kinks is straight. Among the major groove protein-bound DNAs, this 'kink-straight-kink' bend contrasts with ordinary 'round bends' (gradual bending between two protein contact sites). The larger kink (43 degrees ) is induced by a novel mechanism, 'phosphate bridging by an arginine-rich helix': the recognition helix with an arginine cluster is inserted perpendicularly into the major groove and bridges the groove through direct interactions with the phosphate groups. The overall bending angle is 59 degrees, which may be important for the centromere-specific chromatin structure.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.06 kDa 
• Atom Count: 2,019 
• Modeled Residue Count: 173 
• Deposited Residue Count: 173 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR CENTROMERE AUTOANTIGEN B	C [auth A]	131	Homo sapiens	Mutation(s): 0  Gene Names: CENP-B
UniProt & NIH Common Fund Data Resources
Find proteins for P07199 (Homo sapiens) Explore P07199  Go to UniProtKB:  P07199
PHAROS:  P07199 GTEx:  ENSG00000125817

Entity ID: 1
Molecule	Chains	Length	Organism	Image
CENP-B BOX DNA	A [auth B]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
CENP-B BOX DNA	B [auth C]	21	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.222 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.374	α = 90
b = 83.374	β = 90
c = 139.021	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-11 
Deposition Author(s): Tanaka, Y., Nureki, O., Kurumizaka, H., Fukai, S., Kawaguchi, S., Ikuta, M., Iwahara, J., Okazaki, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2002-01-11
  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: 2024-02-07
  Changes: Data collection, Database references