1HLV | PD0192 - JenaLib

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

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)

Date :   04 Dec 00 (Deposition) - 11 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Helix-Turn-Helix, Protein-Dna Complex, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tanaka, O. Nureki, H. Kurumizaka, S. Fukai, S. Kawaguchi, M. Ikuta, J. Iwahara, T. Okazaki, S. Yokoyama
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. V. 20 6612 2001
PubMed-ID: 11726497 | Reference-DOI: 10.1093/EMBOJ/20.23.6612
(for further references see the PDB file header)

Compounds

Molecule 1 - CENP-B BOX DNA
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synthetic	:	YES

Molecule 2 - CENP-B BOX DNA
	Chains	:	C
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synthetic	:	YES

Molecule 3 - MAJOR CENTROMERE AUTOANTIGEN B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15D
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN
	Gene	:	CENP-B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CENP-B

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (1, 1)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:131
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
          CENPB_HUMAN     1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRHG 131
               SCOP domains d1hlva1 A:1-66                                                    d1hlva2 A:67-131                                                  SCOP domains
               CATH domains --------1hlvA01 A:9-66 Homeodomain-like                           -----1hlvA02 A:72-131 Homeodomain-like                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_PSQ  PDB: A:1-52 UniProt: 1-52                  ------------HTH_CENPB  PDB: A:65-129 UniProt: 65-136                            PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-131 UniProt: 1-668 [INCOMPLETE]                                                                                  Transcript 1
                 1hlv A   1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRRS 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:DNA  Length:21
                                                     
                 1hlv B   1 GCCTTCGTTGGAAACGGGATT  21
                                    10        20

Chain C from PDB  Type:DNA  Length:21
                                                     
                 1hlv C   1 AATCCCGTTTCCAACGAAGGC  21
                                    10        20

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CENPB_HUMAN | P07199)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0019237	centromeric DNA binding	Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0003696	satellite DNA binding	Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1hlv)

	Sites
(no "Sites" information available for 1hlv)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hlv)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1hlv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CENPB_HUMAN \| P07199
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CENPB_HUMAN \| P07199
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description