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(-) Description

Title :  SOLUTION STRUCTURE OF THE HMG-BOX DOMAIN IN THE SSRP1 SUBUNIT OF FACT
 
Authors :  N. Kasai, Y. Tsunaka, I. Ohki, S. Hirose, K. Morikawa, S. Tate
Date :  26 Jan 05  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Fact, Ssrp1, Hmg, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kasai, Y. Tsunaka, I. Ohki, S. Hirose, K. Morikawa, S. Tate
Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact
J. Biomol. Nmr V. 32 83 2005
PubMed-ID: 16041486  |  Reference-DOI: 10.1007/S10858-005-3662-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SINGLE-STRAND RECOGNITION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 5-74
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: SSRP1, SSRP, CHORION-FACTOR 5

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1WXL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WXL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.SSRP1_DROME555-621  1A:5-71

(-) Exons   (0, 0)

(no "Exon" information available for 1WXL)

(-) 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:73
 aligned with SSRP1_DROME | Q05344 from UniProtKB/Swiss-Prot  Length:723

    Alignment length:73
                                   561       571       581       591       601       611       621   
          SSRP1_DROME   552 SGKPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWEDAAAKDKQRYHDEMRNYKPEA 624
               SCOP domains d1wxla_ A: automated matches                                              SCOP domains
               CATH domains 1wxlA00 A:2-74 DNA Binding (I), subunit A                                 CATH domains
               Pfam domains ---HMG_box-1wxlA01 A:5-71                                             --- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: A:5-71 UniProt: 555-621                            --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 1wxl A   2 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWEDAAAKDKQRYHDEMRNYKPEA  74
                                    11        21        31        41        51        61        71
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HMG-box (15)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (SSRP1_DROME | Q05344)
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:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    GO:0031491    nucleosome binding    Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0030707    ovarian follicle cell development    The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. An example of this is found in Drosophila melanogaster.
    GO:0051101    regulation of DNA binding    Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0001672    regulation of chromatin assembly or disassembly    Any process that modulates the frequency, rate or extent of chromatin assembly or disassembly.
    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:0035101    FACT complex    An abundant nuclear complex, which was originally identified in mammalian systems as a factor required for transcription elongation on chromatin templates. The FACT complex has been shown to destablilize the interaction between the H2A/H2B dimer and the H3/H4 tetramer of the nucleosome, thus reorganizing the structure of the nucleosome. In this way, the FACT complex may play a role in DNA replication and other processes that traverse the chromatin, as well as in transcription elongation. FACT is composed of two proteins that are evolutionarily conserved in all eukaryotes and homologous to mammalian Spt16 and SSRP1. In metazoans, the SSRP1 homolog contains an HMG domain; however in fungi and protists, it does not. For example, in S. cerevisiae the Pob3 protein is homologous to SSRP1, but lacks the HMG chromatin binding domain. Instead, the yFACT complex of Spt16p and Pob3p, binds to nucleosomes where multiple copies of the HMG-domain containing protein Nhp6p have already bound, but Nhp6p does not form a stable complex with the Spt16p/Pob3p heterodimer.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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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