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(-) Description

Authors :  C. M. Read, P. D. Cary, C. Crane-Robinson, P. C. Driscoll, M. O. M. Carillo, D. G. Norman
Date :  17 Nov 94  (Deposition) - 07 Feb 95  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  C. M. Read, P. D. Cary, C. Crane-Robinson, P. C. Driscoll, M. O. M. Carillo, D. G. Norman
The Structure Of The Hmg Box And Its Interaction With Dna
Nucleic Acids Mol. Biol. V. 9 222 1995
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System StrainDH5 ALPHA
    Expression System Taxid562
    Expression System Vector TypePGEX-2T
    Organism CommonCHINESE HAMSTER
    Organism ScientificCRICETULUS GRISEUS
    Organism Taxid10029

 Structural Features

(-) Chains, Units

NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1NHM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

NMR Structure
1Asp A:79 -Ala A:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.HMGB1_CRIGR60-128

(-) Exons   (0, 0)

(no "Exon" information available for 1NHM)

(-) 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:79
 aligned with HMGB1_CRIGR | P07156 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:79
                                    67        77        87        97       107       117       127         
               SCOP domains d1nhma_ A: High mobility group protein 1, HMG1                                  SCOP domains
               CATH domains 1nhmA00 A:3-81 DNA Binding (I), subunit A                                       CATH domains
               Pfam domains --HMG_box-1nhmA01 A:5-73                                               -------- Pfam domains
         Sec.struct. author .........hhhhhhh..hhhhhh......hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HMG_BOX_2  PDB: A:5-73 UniProt: 60-128                               -------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                                    12        22        32        42        52        62        72         

   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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure
Clan: HMG-box (15)

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (HMGB1_CRIGR | P07156)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
biological process
    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: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:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    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:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0017055    negative regulation of RNA polymerase II transcriptional preinitiation complex assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
    GO:0097350    neutrophil clearance    The selective elimination of senescent neutrophils from the body by autoregulatory mechanisms.
    GO:0051106    positive regulation of DNA ligation    Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
    GO:0034165    positive regulation of toll-like receptor 9 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 9 signaling pathway.
    GO:0002840    regulation of T cell mediated immune response to tumor cell    Any process that modulates the frequency, rate, or extent of a T cell mediated immune response to tumor cell.
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:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.


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    Asp A:79 - Ala A:80   [ RasMol ]  

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 Related Entries

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

        HMGB1_CRIGR | P071561hsm 1hsn 1nhn

(-) Related Entries Specified in the PDB File