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(-) Description

Title :  SOLUTION STRUCTURE OF ETO-TAFH REFINED IN EXPLICIT SOLVENT
 
Authors :  Y. Wei, S. Liu, J. Lausen, C. Woodrell, S. Cho, N. Biris, N. Kobayashi, S. Yokoyama, M. H. Werner
Date :  27 Apr 07  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Transcriptional Cofactor, Leukemia, 4-Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wei, S. Liu, J. Lausen, C. Woodrell, S. Cho, N. Biris, N. Kobayashi, Y. Wei, S. Yokoyama, M. H. Werner
A Taf4-Homology Domain From The Corepressor Eto Is A Docking Platform For Positive And Negative Regulators Of Transcription
Nat. Struct. Mol. Biol. V. 14 653 2007
PubMed-ID: 17572682  |  Reference-DOI: 10.1038/NSMB1258
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN ETO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: TAFH DOMAIN, RESIDUES 119-225
    Gene: RUNX1T1, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN CBFA2T1, PROTEIN MTG8, EIGHT TWENTY ONE PROTEIN, CYCLIN-D-RELATED PROTEIN, ZINC FINGER MYND DOMAIN- CONTAINING PROTEIN 2

 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 2PP4)

(-) Sites  (0, 0)

(no "Site" information available for 2PP4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PP4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PP4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PP4)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TAFHPS51119 TAFH/NHR1 domain profile.MTG8_HUMAN120-215  1A:120-215

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6bENST000002658146bENSE00001297181chr8:93088364-93088193172MTG8_HUMAN1-30300--
1.11lENST0000026581411lENSE00001782570chr8:93029591-93029454138MTG8_HUMAN30-76470--
1.12nENST0000026581412nENSE00002197259chr8:93027048-93026807242MTG8_HUMAN76-156811A:119-15638
1.13cENST0000026581413cENSE00001682869chr8:93023319-9302323090MTG8_HUMAN157-186301A:157-18630
1.14eENST0000026581414eENSE00001706185chr8:93017525-93017344182MTG8_HUMAN187-247611A:187-22539
1.17bENST0000026581417bENSE00001739575chr8:93004117-93003867251MTG8_HUMAN247-331850--
1.18bENST0000026581418bENSE00001770404chr8:92999200-9299911586MTG8_HUMAN331-359290--
1.19ENST0000026581419ENSE00001764658chr8:92998553-92998352202MTG8_HUMAN360-427680--
1.21ENST0000026581421ENSE00001658814chr8:92988201-9298813369MTG8_HUMAN427-450240--
1.22cENST0000026581422cENSE00001768415chr8:92983076-92982886191MTG8_HUMAN450-513640--
1.23hENST0000026581423hENSE00001226380chr8:92972745-929711521594MTG8_HUMAN514-604910--

(-) 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 MTG8_HUMAN | Q06455 from UniProtKB/Swiss-Prot  Length:604

    Alignment length:107
                                   128       138       148       158       168       178       188       198       208       218       
           MTG8_HUMAN   119 GARQLSKLKRFLTTLQQFGNDISPEIGERVRTLVLGLVNSTLTIEEFHSKLQEATNFPLRPFVIPFLKANLPLLQRELLHCARLAKQNPAQYLAQHEQLLLDASTTS 225
               SCOP domains d2pp4a1 A:119-225 ETO                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -TAFH-2pp4A01 A:120-215                                                                          ---------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TAFH  PDB: A:120-215 UniProt: 120-215                                                           ---------- PROSITE
               Transcript 1 Exon 1.12n  PDB: A:119-156            Exon 1.13c  PDB: A:157-186    Exon 1.14e  PDB: A:187-225 [INCOMPLETE] Transcript 1
                 2pp4 A 119 GARQLSKLKRFLTTLQQYGNDISPEIGERVRTLVLGLVNSTLTIEEFHSKLQEATNFPLRPFVIPFLKANLPLLQRELLHCARLAKQNPAQYLAQHEQLLLDASTTS 225
                                   128       138       148       158       168       178       188       198       208       218
   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  (0, 0)

(no "CATH Domain" information available for 2PP4)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: TAFH] (3)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (MTG8_HUMAN | Q06455)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
    GO:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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
        MTG8_HUMAN | Q06455: 1wq6 2dj8 2h7b 2knh 2kyg 2od1 2odd 4jol

(-) Related Entries Specified in the PDB File

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