2EQZ - JenaLib

Title :   SOLUTION STRUCTURE OF THE FIRST HMG-BOX DOMAIN FROM HIGH MOBILITY GROUP PROTEIN B3

Authors :   X. R. Qin, C. Kurosaki, M. Yoshida, F. Hayahsi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Mar 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Hmg-Box Domain, High Mobility Group Protein B3, Mobility Group Protein 4, Mobility Group Protein 2A, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. R. Qin, C. Kurosaki, M. Yoshida, F. Hayashi, S. Yokoyama
Solution Structure Of The First Hmg-Box Domain From High Mobility Group Protein B3
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

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 (2, 2)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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

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Chain A from PDB  Type:PROTEIN  Length:86
 aligned with HMGB3_HUMAN | O15347 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:86
                                   1                                                                              
                                   | 3        13        23        33        43        53        63        73      
           HMGB3_HUMAN    - -------MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG 79
               SCOP domains d2eqza_ A: automated matches                                                           SCOP domains
               CATH domains 2eqzA00 A:1-86 DNA Binding (I), subunit A                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------A----Q----------------------- SAPs(SNPs)
                PROSITE (1) ---------------HMG_BOX_2  PDB: A:16-86 UniProt: 9-79                                   PROSITE (1)
                PROSITE (2) -----------------------------------------------HMG_BOX_1   --------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2eqz A  1 GSSGSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG 86
                                    10        20        30        40        50        60        70        80

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

NMR Structure(hide GO term definitions)

Chain A (HMGB3_HUMAN | O15347)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008301	DNA binding, bending	The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0000400	four-way junction DNA binding	Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
	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:0032392	DNA geometric change	The process in which a transformation is induced in the geometry of a DNA double helix, resulting in a change in twist, writhe, or both, but with no change in linking number. Includes the unwinding of double-stranded DNA by helicases.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	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:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0045596	negative regulation of cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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