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(-) Description

Title :  SOLUTION STRUCTURE OF THE MYND DOMAIN FROM AML1-ETO COMPLEXED WITH SMRT, A COREPRESSOR
 
Authors :  Y. Z. Liu, W. Chen, J. Gaudet, M. D. Cheney, L. Roudaia, T. Cierpicki, R. C. Klet, K. Hartman, T. M. Laue, N. A. Speck, J. H. Bushweller
Date :  22 Dec 06  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (25x)
Keywords :  Mynd Zinc Finger, Cross-Braced Topology, Poly-Proline, Proline-Tryptophan Interaction, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Liu, W. Chen, J. Gaudet, M. D. Cheney, L. Roudaia, T. Cierpicki, R. C. Klet, K. Hartman, T. M. Laue, N. A. Speck, J. H. Bushweller
Structural Basis For Recognition Of Smrt/N-Cor By The Mynd Domain And Its Contribution To Aml1/Eto'S Activity.
Cancer Cell V. 11 483 2007
PubMed-ID: 17560331  |  Reference-DOI: 10.1016/J.CCR.2007.04.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMRT
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T3
    Expression System StrainBL-21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSMRT (RESIDUES 1101-1113)
    GeneSMRT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - PROTEIN CBFA2T1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX4T3
    Expression System StrainBL-21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentMYND DOMAIN (AML1-ETO, RESIDUES 658-707)
    GeneAML1-ETO
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN MTG8, PROTEIN ETO, EIGHT TWENTY ONE PROTEIN, CYCLIN-D-RELATED PROTEIN, ZINC FINGER MYND DOMAIN- CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:663 , CYS A:666 , CYS A:683 , CYS A:687BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:674 , CYS A:677 , HIS A:695 , CYS A:699BINDING SITE FOR RESIDUE ZN A 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 1)

NMR Structure (2, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_MYND_1PS01360 Zinc finger MYND-type signature.MTG8_HUMAN515-551  1A:663-699
2ZF_MYND_2PS50865 Zinc finger MYND-type profile.MTG8_HUMAN515-551  1A:663-699

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6bENST000002658146bENSE00001297181chr8:93088364-93088193172MTG8_HUMAN1-30300--
1.11lENST0000026581411lENSE00001782570chr8:93029591-93029454138MTG8_HUMAN30-76470--
1.12nENST0000026581412nENSE00002197259chr8:93027048-93026807242MTG8_HUMAN76-156810--
1.13cENST0000026581413cENSE00001682869chr8:93023319-9302323090MTG8_HUMAN157-186300--
1.14eENST0000026581414eENSE00001706185chr8:93017525-93017344182MTG8_HUMAN187-247610--
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_HUMAN450-513641A:658-6614
1.23hENST0000026581423hENSE00001226380chr8:92972745-929711521594MTG8_HUMAN514-604911A:662-70746

(-) 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:50
 aligned with MTG8_HUMAN | Q06455 from UniProtKB/Swiss-Prot  Length:604

    Alignment length:50
                                   519       529       539       549       559
          MTG8_HUMAN    510 DSSESCWNCGRKASETCSGCNTARYCGSFCQHKDWEKHHHICGQTLQAQQ  559
               SCOP domains d2odda_ A: automated matches                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -----zf-MYND-2oddA01 A:663-699            -------- Pfam domains
         Sec.struct. author ..............eee......ee.hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ZF_MYND_1  PDB: A:663-699            -------- PROSITE (1)
                PROSITE (2) -----ZF_MYND_2  PDB: A:663-699            -------- PROSITE (2)
               Transcript 1 1.22Exon 1.23h  PDB: A:662-707 UniProt: 514-604    Transcript 1
                2odd A  658 DSSESCWNCGRKASETCSGCNTARYCGSFCQHKDWEKHHHICGQTLQAQQ  707
                                   667       677       687       697       707

Chain B from PDB  Type:PROTEIN  Length:13
 aligned with NCOR2_HUMAN | Q9Y618 from UniProtKB/Swiss-Prot  Length:2525

    Alignment length:13
                                  1118   
         NCOR2_HUMAN   1109 TISNPPPLISSAK 1121
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .......eee... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                2odd B 1101 TISNPPPLISSAK 1113
                                  1110   

   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  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: TRASH (61)

(-) Gene Ontology  (29, 37)

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.

Chain B   (NCOR2_HUMAN | Q9Y618)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005112    Notch binding    Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:1903799    negative regulation of production of miRNAs involved in gene silencing by miRNA    Any process that stops, prevents or reduces the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
    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:0072365    regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTG8_HUMAN | Q064551wq6 2dj8 2h7b 2knh 2kyg 2od1 2pp4 4jol
        NCOR2_HUMAN | Q9Y6181kkq 1r2b 1xc5 2gpv 2l5g 2ltp 2rt5 3r29 3r2a 4a69 4oar 5x8q 5x8x

(-) Related Entries Specified in the PDB File

2od1