3EYI - JenaLib

Title :   THE CRYSTAL STRUCTURE OF THE SECOND Z-DNA BINDING DOMAIN OF HUMAN DAI (ZBP1) IN COMPLEX WITH Z-DNA

Authors :   S. C. Ha, K. K. Kim

Date :   21 Oct 08 (Deposition) - 13 Jan 09 (Release) - 13 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Alternative Splicing, Dna-Binding, Polymorphism, Dna Binding Protein/Z-Dna Complex, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Ha, D. Kim, H. Y. Hwang, A. Rich, Y. G. Kim, K. K. Kim
The Crystal Structure Of The Second Z-Dna Binding Domain Of Human Dai (Zbp1) In Complex With Z-Dna Reveals An Unusual Binding Mode To Z-Dna.
Proc. Natl. Acad. Sci. Usa V. 105 20671 2008
PubMed-ID: 19095800 | Reference-DOI: 10.1073/PNAS.0810463106
(for further references see the PDB file header)

Compounds

Molecule 1 - Z-DNA-BINDING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	THE SECOND Z-DNA BINDING DOMAIN (ZBETA)
	Gene	:	C20ORF183, DLM1, ZBP1, ZBP1/DLM1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TUMOR STROMA AND ACTIVATED MACROPHAGE PROTEIN DLM- 1

Molecule 2 - 5'-TCGCGCG-3'
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THE Z-DNA IS CHEMICALLY SYNTHESIZED.
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:64
 aligned with ZBP1_HUMAN | Q9H171 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:64
                                   111       121       131       141       151       161    
           ZBP1_HUMAN   102 GPQFSQQREEDIYRFLKDNGPQRALVIAQALGMRTAKDVNRDLYRMKSRHLLDMDEQSKAWTIY 165
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.eehhhhhhhh...hhhhhhhhhhhhhhh..eee.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------H----------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 3eyi A  -1 SPQFSQQREEDIYRFLKDNGPQRALVIAQALGMRTAKDVNRDLYRMKSRHLLDMDEQSKAWTIY 165
                            ||     111       121       131       141       151       161    
                            ||                                                              
                           -1|                                                              
                           103

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with ZBP1_HUMAN | Q9H171 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:73
                                   102       112       122       132       142       152       162   
           ZBP1_HUMAN    93 HAATIPETPGPQFSQQREEDIYRFLKDNGPQRALVIAQALGMRTAKDVNRDLYRMKSRHLLDMDEQSKAWTIY 165
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------....hhhhhhhhhhhhhhh.eehhhhhhhh...hhhhhhhhhhhhhhh..eee.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------H----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 3eyi B  -4 HMAS------PQFSQQREEDIYRFLKDNGPQRALVIAQALGMRTAKDVNRDLYRMKSRHLLDMDEQSKAWTIY 165
                               |     -|      112       122       132       142       152       162   
                              -1    103

Chain C from PDB  Type:DNA  Length:6
                                      
                 3eyi C   1 CGCGCG   6

Chain D from PDB  Type:DNA  Length:7
                                       
                 3eyi D   0 TCGCGCG   6

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ZBP1_HUMAN | Q9H171)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003726	double-stranded RNA adenosine deaminase activity	Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule.
	GO:0003692	left-handed Z-DNA binding	Interacting selectively and non-covalently with DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0032481	positive regulation of type I interferon production	Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

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	Cis Peptide Bonds
		Gly B:121 - Pro B:122	[ RasMol ]
		Ser B:-1 - Pro B:103	[ RasMol ]

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