PDBsum entry 1hlv

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protein dna_rna links
DNA binding protein/DNA PDB id
Protein chain
131 a.a. *
Waters ×98
* Residue conservation analysis
PDB id:
Name: DNA binding protein/DNA
Title: Crystal structure of cenp-b(1-129) complexed with the cenp- b box DNA
Structure: Cenp-b box DNA. Chain: b. Engineered: yes. Cenp-b box DNA. Chain: c. Engineered: yes. Major centromere autoantigen b. Chain: a. Fragment: DNA binding domain.
Source: Synthetic: yes. Other_details: this sequence occurs naturally in humans.. Homo sapiens. Human. Organism_taxid: 9606. Gene: cenp-b. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
2.50Å     R-factor:   0.222     R-free:   0.260
Authors: Y.Tanaka,O.Nureki,H.Kurumizaka,S.Fukai,S.Kawaguchi,M.Ikuta, J.Iwahara,T.Okazaki,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
Y.Tanaka et al. (2001). 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. PubMed id: 11726497 DOI: 10.1093/emboj/20.23.6612
04-Dec-00     Release date:   11-Jan-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07199  (CENPB_HUMAN) -  Major centromere autoantigen B
599 a.a.
131 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     1 term  


DOI no: 10.1093/emboj/20.23.6612 EMBO J 20:6612-6618 (2001)
PubMed id: 11726497  
Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
Y.Tanaka, O.Nureki, H.Kurumizaka, S.Fukai, S.Kawaguchi, M.Ikuta, J.Iwahara, T.Okazaki, S.Yokoyama.
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.
  Selected figure(s)  
Figure 2.
Figure 2 Protein -DNA interactions. (A) Schematic diagram summarizing the DNA contacts by CENP-B[1 -129]. The essential base pairs in sites 1, 2 and 3 are colored blue. Water molecules are denoted as open circles labeled with W. Open circles represent phosphates. Hydrogen bonds and salt bridges with the backbone phosphate groups are indicated with thick black lines. Specific recognitions of bases in sites 1, 2 and 3 are shown in red (hydrogen bonds) and yellow (van der Waals interactions) lines. (B -D) Specific interactions at sites 1, 2 and 3, respectively (stereo view). DNA strands are shown in green and yellow. Dotted lines in gray represent hydrogen bonds, and those in orange represent van der Waals interactions. (E) Graphic representation of the widths of the major and minor grooves, calculated by CURVES (Lavery et al., 1988). The vertical axis indicates the groove width (Å) and the horizontal axis indicates the base number. The solid and dashed lines indicate the widths of the major and minor grooves, respectively.
Figure 4.
Figure 4 Schematic drawings of DNA structures in the complexes with CENP-B (A), CAP (B), MATa1/MAT 2 (C) and SRF (D). Cylinders indicate recognition helices for DNA binding. The 3' and 5' ends of DNA molecules are indicated by open and closed circles, respectively. The complex with CAP contains two molecules of double-stranded DNA, which has a four base overhang at the 3' end, and the complexes with CENP-B, MATa1/MAT 2 and SRF contain one molecule of double-stranded DNA.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 6612-6618) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23135398 S.P.Montaño, Y.Z.Pigli, and P.A.Rice (2012).
The Mu transpososome structure sheds light on DDE recombinase evolution.
  Nature, 491, 413-417.
PDB code: 4fcy
20008103 R.D.Hutton, T.D.Craggs, M.F.White, and J.C.Penedo (2010).
PCNA and XPF cooperate to distort DNA substrates.
  Nucleic Acids Res, 38, 1664-1675.  
19656849 M.Anderson, J.Haase, E.Yeh, and K.Bloom (2009).
Function and assembly of DNA looping, clustering, and microtubule attachment complexes within a eukaryotic kinetochore.
  Mol Biol Cell, 20, 4131-4139.  
19336418 S.Orthaus, K.Klement, N.Happel, C.Hoischen, and S.Diekmann (2009).
Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins.
  Nucleic Acids Res, 37, 3391-3406.  
17940212 C.Casola, D.Hucks, and C.Feschotte (2008).
Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals.
  Mol Biol Evol, 25, 29-41.  
18072184 S.Orthaus, C.Biskup, B.Hoffmann, C.Hoischen, S.Ohndorf, K.Benndorf, and S.Diekmann (2008).
Assembly of the inner kinetochore proteins CENP-A and CENP-B in living human cells.
  Chembiochem, 9, 77-92.  
17595300 G.Lerman, and B.E.Shakhnovich (2007).
Defining functional distance using manifold embeddings of gene ontology annotations.
  Proc Natl Acad Sci U S A, 104, 11334-11339.  
17992470 N.K.Lee, A.Johner, and S.C.Hong (2007).
Compressing a rigid filament: Buckling and cyclization.
  Eur Phys J E Soft Matter, 24, 229-241.  
17130173 M.M.Babu, L.M.Iyer, S.Balaji, and L.Aravind (2006).
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.
  Nucleic Acids Res, 34, 6505-6520.  
17115329 M.Rosandić, V.Paar, I.Basar, M.Gluncić, N.Pavin, and I.Pilas (2006).
CENP-B box and pJalpha sequence distribution in human alpha satellite higher-order repeats (HOR).
  Chromosome Res, 14, 735-753.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15634350 Y.Tanaka, H.Kurumizaka, and S.Yokoyama (2005).
CpG methylation of the CENP-B box reduces human CENP-B binding.
  FEBS J, 272, 282-289.  
16183641 Y.Tanaka, H.Tachiwana, K.Yoda, H.Masumoto, T.Okazaki, H.Kurumizaka, and S.Yokoyama (2005).
Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences.
  J Biol Chem, 280, 41609-41618.  
14522975 M.S.Tawaramoto, S.Y.Park, Y.Tanaka, O.Nureki, H.Kurumizaka, and S.Yokoyama (2003).
Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution.
  J Biol Chem, 278, 51454-51461.
PDB code: 1ufi
12682358 N.Fujikawa, H.Kurumizaka, O.Nureki, T.Terada, M.Shirouzu, T.Katayama, and S.Yokoyama (2003).
Structural basis of replication origin recognition by the DnaA protein.
  Nucleic Acids Res, 31, 2077-2086.
PDB code: 1j1v
12566397 S.E.Hall, G.Kettler, and D.Preuss (2003).
Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains.
  Genome Res, 13, 195-205.  
12773553 W.Liu, J.Seto, E.Sibille, and M.Toth (2003).
The RNA binding domain of Jerky consists of tandemly arranged helix-turn-helix/homeodomain-like motifs and binds specific sets of mRNAs.
  Mol Cell Biol, 23, 4083-4093.  
12130537 H.Nakagawa, J.K.Lee, J.Hurwitz, R.C.Allshire, J.Nakayama, S.I.Grewal, K.Tanaka, and Y.Murakami (2002).
Fission yeast CENP-B homologs nucleate centromeric heterochromatin by promoting heterochromatin-specific histone tail modifications.
  Genes Dev, 16, 1766-1778.  
11956223 I.M.Cheeseman, D.G.Drubin, and G.Barnes (2002).
Simple centromere, complex kinetochore: linking spindle microtubules and centromeric DNA in budding yeast.
  J Cell Biol, 157, 199-203.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.