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(-) Description

Authors :  B. Kim, K. -S. Ryu, H. J. Kim, B. -S. Choi
Date :  27 Jun 03  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hhr23B, Xpc Binding Domain, Nmr Solution Structure, Nucleotide Excision Repair, Chaps, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  B. Kim, K. S. Ryu, H. J. Kim, S. J. Cho, B. S. Choi
Solution Structure And Backbone Dynamics Of The Xpc-Binding Domain Of The Human Dna Repair Protein Hhr23B.
Febs J. V. 272 2467 2005
PubMed-ID: 15885096  |  Reference-DOI: 10.1111/J.1742-4658.2005.04667.X
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PVE)

(-) Sites  (0, 0)

(no "Site" information available for 1PVE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PVE)

(-) Cis Peptide Bonds  (4, 6)

NMR Structure
18, 19Gly A:71 -Gly A:72
29, 19Gly A:67 -Gln A:68
316Ser A:2 -His A:3
419Glu A:64 -Ala A:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PVE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PVE)

(-) Exons   (3, 3)

NMR Structure (3, 3)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

NMR Structure
   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:72
 aligned with RD23B_HUMAN | P54727 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:72
                            274 |                                                                   
                              | |  280       290       300       310       320       330       340  
               SCOP domains d1pvea_ A: XPC-binding domain of Rad23 homolog B (Hhr23b)                SCOP domains
               CATH domains 1pveA00 A:1-72 XPC-binding domain                                        CATH domains
               Pfam domains -----XPC-binding-1pveA01 A:6-64                                 -------- Pfam domains
         Sec.struct. author .....hhhhh......hhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.-------------------------------------------Exon 1.10a  PDB: A:46-72    Transcript 1 (1)
           Transcript 1 (2) -Exon 1.9  PDB: A:2-45 UniProt: 273-315      --------------------------- Transcript 1 (2)
                                    10        20        30        40        50        60        70  

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  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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (RD23B_HUMAN | P54727)
molecular function
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    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).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0000715    nucleotide-excision repair, DNA damage recognition    The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix.
    GO:0000717    nucleotide-excision repair, DNA duplex unwinding    The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
    GO:0006294    nucleotide-excision repair, preincision complex assembly    The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0032434    regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that modulates the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0071942    XPC complex    A nucleotide-excision repair complex that is involved in damage sensing during global genome nucleotide excision repair (GG-NER). It is part of the pre-incision (or initial recognition) complex bound to sites of DNA damage. In human, it is composed of XPC, RAD23B and CETN2.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.


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    Glu A:64 - Ala A:65   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        RD23B_HUMAN | P547271p1a 1uel

(-) Related Entries Specified in the PDB File

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