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(-) Description

Title :  IMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN
 
Authors :  T. Nagata, V. Gupta, D. Sorce, W. Y. Kim, A. Sali, B. T. Chait, K. Shigesada, Y. Ito, M. H. Werner
Date :  11 May 99  (Deposition) - 05 Jan 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (43x)
Keywords :  Transcription Factor, Hematopoiesis, Osteogenesis, Ig-Fold, Nmr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nagata, V. Gupta, D. Sorce, W. Y. Kim, A. Sali, B. T. Chait, K. Shigesada, Y. Ito, M. H. Werner
Immunoglobulin Motif Dna Recognition And Heterodimerization Of The Pebp2/Cbf Runt Domain.
Nat. Struct. Biol. V. 6 615 1999
PubMed-ID: 10404214  |  Reference-DOI: 10.1038/10658
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYOMAVIRUS ENHANCER BINDING PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Cellular Location: CYTOPLASM
    Expression System Plasmid: PQE9
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: CORE-BINDING FACTOR ALPHA B SUBUNIT, RUNT DOMAIN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACUTE MYELOID LEUKEMIA 1 PROTEIN, AML1/OSF2, PEBP2-ALPHA B

 Structural Features

(-) Chains, Units

  
NMR Structure (43x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1CMO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012128R139QRUNX1_HUMANDisease (FPDMM)  ---AR139Q
2UniProtVAR_012129R174QRUNX1_HUMANDisease (FPDMM)74315450AR174Q
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CMO)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.18aENST0000034469118aENSE00001380483chr21:36260987-362591401848RUNX1_HUMAN1-90901A:52-9039
1.19cENST0000034469119cENSE00001660291chr21:36253010-36252854157RUNX1_HUMAN91-143531A:91-14353
1.20aENST0000034469120aENSE00002199204chr21:36231875-36231771105RUNX1_HUMAN143-178361A:143-17836
1.22aENST0000034469122aENSE00002198909chr21:36206898-36206707192RUNX1_HUMAN178-242651A:178-1781
1.25ENST0000034469125ENSE00002149931chr21:36171759-36171598162RUNX1_HUMAN242-296550--
1.26eENST0000034469126eENSE00001623427chr21:36164907-361600984810RUNX1_HUMAN296-4531580--

(-) 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:127
 aligned with RUNX1_HUMAN | Q01196 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:127
                                    61        71        81        91       101       111       121       131       141       151       161       171       
          RUNX1_HUMAN    52 VEVLADHPGELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRR 178
               SCOP domains d1cmoa_ A: Acute myeloid leukemia 1 protein (AML1), RUNT domain                                                                 SCOP domains
               CATH domains 1cmoA00 A:52-178  [code=2.60.40.720, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.....ee.....eeee....eee........eeeee......eeeeeeeeee....eeeee..eeeee..eeee...eeeee......eeeeeee.....eeeeeee..eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------Q----------------------------------Q---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18a  PDB: A:52-90 UniProt: 1-90 Exon 1.19c  PDB: A:91-143 UniProt: 91-143            ----------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------Exon 1.20a  PDB: A:143-178           Transcript 1 (2)
                 1cmo A  52 VEVLADHPGELVRTDSPNFLCSVLPTHWRSNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRR 178
                                    61        71        81        91       101       111       121       131       141       151       161       171
   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 beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (RUNX1_HUMAN | Q01196)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. 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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0000975    regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
    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.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0002062    chondrocyte differentiation    The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0071425    hematopoietic stem cell proliferation    The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    GO:0030853    negative regulation of granulocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0048935    peripheral nervous system neuron development    The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0030854    positive regulation of granulocyte differentiation    Any process that activates or increases the frequency, rate or extent of granulocyte differentiation.
    GO:0032743    positive regulation of interleukin-2 production    Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases 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:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma 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

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UniProtKB/Swiss-Prot
        RUNX1_HUMAN | Q01196: 1co1 1e50 1h9d 1ljm

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