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(-) Description

Title :  HUMAN MRF-2 DOMAIN, NMR, 11 STRUCTURES
 
Authors :  D. Lin, V. Tsui, D. Case, Y. C. Yuan, Y. Chen
Date :  17 Apr 01  (Deposition) - 25 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (11x)
Keywords :  Dna Binding Protein, Mrf-2, Dna-Binding Motif, Protein-Dna Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lin, V. Tsui, D. Case, Y. C. Yuan, Y. Chen
Human Mrf-2 Domain, Nmr, 11 Structures
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MODULATOR RECOGNITION FACTOR 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQE30
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN
    Gene: MRF-2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MRF-2

 Structural Features

(-) Chains, Units

  
NMR Structure (11x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IG6)

(-) Sites  (0, 0)

(no "Site" information available for 1IG6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IG6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IG6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IG6)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARIDPS51011 ARID domain profile.ARI5B_HUMAN318-410  1A:1-93

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002798731aENSE00001879709chr10:63661059-63661489431ARI5B_HUMAN1-770--
1.2ENST000002798732ENSE00001179149chr10:63661918-63662172255ARI5B_HUMAN8-92850--
1.3ENST000002798733ENSE00001179143chr10:63699942-63700167226ARI5B_HUMAN93-168760--
1.4ENST000002798734ENSE00001274896chr10:63759850-63760080231ARI5B_HUMAN168-245780--
1.6aENST000002798736aENSE00001274844chr10:63810647-63810759113ARI5B_HUMAN245-282380--
1.7ENST000002798737ENSE00001274882chr10:63816876-63817077202ARI5B_HUMAN283-350681A:1-3333
1.8ENST000002798738ENSE00000994546chr10:63819002-6381905453ARI5B_HUMAN350-367181A:33-5018
1.9ENST000002798739ENSE00000994549chr10:63829459-6382955698ARI5B_HUMAN368-400331A:51-8333
1.10ENST0000027987310ENSE00000994550chr10:63845461-63845659199ARI5B_HUMAN400-466671A:83-10725
1.11bENST0000027987311bENSE00001461591chr10:63850621-638567036083ARI5B_HUMAN467-11887220--

(-) 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:107
 aligned with ARI5B_HUMAN | Q14865 from UniProtKB/Swiss-Prot  Length:1188

    Alignment length:107
                                   327       337       347       357       367       377       387       397       407       417       
          ARI5B_HUMAN   318 RADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERLILPYERFIKGEEDKPLPPIKPRK 424
               SCOP domains d1ig6a_ A: MRF-2 DNA-binding domain                                                                         SCOP domains
               CATH domains 1ig6A00 A:1-107  [code=1.10.150.60, no name defined]                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh..hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ARID  PDB: A:1-93 UniProt: 318-410                                                           -------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:1-33            -------------------------------------------------Exon 1.10  PDB: A:83-107  Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.8          Exon 1.9  PDB: A:51-83           ------------------------ Transcript 1 (2)
                 1ig6 A   1 RADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERLILPYERFIKGEEDKPLPPIKPRK 107
                                    10        20        30        40        50        60        70        80        90       100
   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  (0, 0)

(no "Pfam Domain" information available for 1IG6)

(-) Gene Ontology  (33, 33)

NMR Structure(hide GO term definitions)
Chain A   (ARI5B_HUMAN | Q14865)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001227    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0060612    adipose tissue development    The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
    GO:0030325    adrenal gland development    The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
    GO:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0060325    face morphogenesis    The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
    GO:0045444    fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
    GO:0060613    fat pad development    The progression of a fat pad from its initial formation to its mature structure. A fat pad is an accumulation of adipose tissue.
    GO:0008585    female gonad development    The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
    GO:0010761    fibroblast migration    Cell migration that is accomplished by extension and retraction of a fibroblast pseudopodium. A fibroblast is a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules.
    GO:0016577    histone demethylation    The modification of histones by removal of methyl groups.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0048644    muscle organ morphogenesis    The process in which the anatomical structures of muscle are generated and organized.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARI5B_HUMAN | Q14865: 2oeh

(-) Related Entries Specified in the PDB File

1bmy 1BMY IS LOW QUALITY STRUCTURE OF HUMAN MRF-2 DOMAIN