1HLV

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

Summary for 1HLV

• Entry DOI: 10.2210/pdb1hlv/pdb
• Related: 1BW6 1IGN 6PAX
• Descriptor: CENP-B BOX DNA, MAJOR CENTROMERE AUTOANTIGEN B, ... (4 entities in total)
• Functional Keywords: helix-turn-helix, protein-dna complex, riken structural genomics/proteomics initiative, rsgi, structural genomics, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P07199
• Total number of polymer chains: 3
• Total formula weight: 28056.05

Authors

Tanaka, Y.,Nureki, O.,Kurumizaka, H.,Fukai, S.,Kawaguchi, S.,Ikuta, M.,Iwahara, J.,Okazaki, T.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2000-12-04, release date: 2002-01-11, Last modification date: 2024-02-07)

Primary citation

Tanaka, Y.,Nureki, O.,Kurumizaka, H.,Fukai, S.,Kawaguchi, S.,Ikuta, M.,Iwahara, J.,Okazaki, T.,Yokoyama, S.
Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
EMBO J., 20:6612-6618, 2001

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.

PubMed: 11726497
DOI: 10.1093/emboj/20.23.6612

Experimental method

X-RAY DIFFRACTION (2.5 Å)