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(-) Description

Title :  CRYSTAL STRUCTURE OF C-MYB R2
 
Authors :  T. H. Tahirov, K. Ogata
Date :  06 Feb 02  (Deposition) - 03 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription, Transcription Regulation, Myb, C-Myb, Dna Binding, Ion Bindi Proto-Oncogene, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Tahirov, H. Morii, H. Uedaira, M. Sasaki, A. Sarai, S. Adachi, S. Y. Park, N. Kamiya, K. Ogata
Crystal Structure Of C-Myb Dna-Binding Domain: Specific Na+ Binding And Correlation With Nmr Structure
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYB PROTO-ONCOGENE PROTEIN
    Chains: A
    Fragment: R2, RESIDUES 90-141
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:119 , LEU A:122 , ARG A:125 , HOH A:2024 , HOH A:2025 , HOH A:2029BINDING SITE FOR RESIDUE NA A1142

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GV5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GV5)

(-) Exons   (0, 0)

(no "Exon" information available for 1GV5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:52
 aligned with MYB_MOUSE | P06876 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:52
                                    99       109       119       129       139  
            MYB_MOUSE    90 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPE 141
               SCOP domains d1gv5a_ A: c-Myb, DNA-binding domain                 SCOP domains
               CATH domains 1gv5A00 A:90-141 Homeodomain-like                    CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 1gv5 A  90 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPE 141
                                    99       109       119       129       139
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GV5)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MYB_MOUSE | P06876)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0071987    WD40-repeat domain binding    Interacting selectively and non-covalently with a WD40 repeat domain of a protein. The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Several of these repeats are combined to form a type of protein domain called the WD domain.
    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: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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter 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:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071354    cellular response to interleukin-6    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 an interleukin-6 stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0048566    embryonic digestive tract development    The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
    GO:0048872    homeostasis of number of cells    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    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: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:0045624    positive regulation of T-helper cell differentiation    Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation.
    GO:0051571    positive regulation of histone H3-K4 methylation    Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
    GO:0051574    positive regulation of histone H3-K9 methylation    Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
    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:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0017145    stem cell division    The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        MYB_MOUSE | P06876: 1guu 1gv2 1gvd 1h88 1h89 1idy 1idz 1mbe 1mbf 1mbg 1mbh 1mbj 1mbk 1mse 1msf 1sb0 2agh

(-) Related Entries Specified in the PDB File

1guu CRYSTAL STRUCTURE OF C-MYB R1
1gv2 CRYSTAL STRUCTURE OF C-MYB R2R3
1h88 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1
1h89 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2
1idy STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZEDAVERAGE STRUCTURE
1idz STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, 20 STRUCTURES
1mbe MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 1
1mbf MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 1
1mbg MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 2
1mbh MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 2
1mbj MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 3
1mbk MOUSE C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN REPEAT 3
1mse C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN COMPLEXED WITH DEOXYRIBONUCLEIC ACID (NMR, MINIMIZED AVERAGE STRUCTURE)
1msf C-MYB DEOXYRIBONUCLEIC ACID-BINDING DOMAIN COMPLEXED WITH DEOXYRIBONUCLEIC ACID (NMR, 25 STRUCTURES)