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Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text Tudor domain, H3K4me3 binding, methylation, GENE REGULATION

    Polymeric Molecules

    Chain A
    Description Spindlin-1 
    Fragment UNP residues 27-262 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 27128.9 
    Source Method genetically manipulated  
    Entity Name Ovarian cancer-related protein 
    Chain B
    Description Histone H3 
    Fragment H3K4(me3) peptide (UNP residues 2-9) 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 976.2 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    SO4  SULFATE ION  O4 S   96.06  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A SPIN1_HUMAN Q9Y657     
    B Q5TEC6_HUMAN Q5TEC6     

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    7275   Multicellular Organismal Development  The Biological Process Whose Specific Outcome Is the Progression of a Multicellular Organism Over Time From an Initial Condition (e.g. a Zygote or a Young Adult) to a Later Condition (e.g. a Multicellular Animal or an Aged Adult). 
    7276   Gamete Generation  The Generation and Maintenance of Gametes in a Multicellular Organism. a Gamete Is a Haploid Reproductive Cell. 
    9303   RRNA Transcription  The Synthesis of Ribosomal RNA (rrna) Any RNA That Forms Part of the Ribosomal Structure From a DNA Template. 
    16055   Wnt Signaling Pathway  The Series of Molecular Signals Initiated by Binding of a Wnt Protein to a Frizzled Family Receptor On the Surface of the Target Cell and Ending with a Change in Cell State. 
    16568   Chromatin Modification  The Alteration of DNA Protein or Sometimes RNA in Chromatin Which May Result in Changing the Chromatin Structure. 
    30177   Positive Regulation of Wnt Signaling Pathway  Any Process That Activates or Increases the Frequency Rate or Extent of Wnt Signal Transduction. 
    51321   Meiotic Cell Cycle  Progression Through the Phases of the Meiotic Cell Cycle in Which Canonically a Cell Replicates to Produce Four Offspring with Half the Chromosomal Content of the Progenitor Cell Via Two Nuclear Divisions. 
    5634   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. 
    5730   Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Cells. It Is Rich in RNA and Protein Is Not Bounded by a Limiting Membrane and Is Not Seen During Mitosis. Its Prime Function Is the Transcription of the Nucleolar DNA Into 45s Ribosomal Precursor RNA the Processing of This RNA Into 5.8s 18s and 28s Components of Ribosomal RNA and the Association of These Components with 5s RNA and Proteins Synthesized Outside the Nucleolus. This Association Results in the Formation of Ribonucleoprotein Precursors; These Pass Into the Cytoplasm and Mature Into the 40s and 60s Subunits of the Ribosome. 
    5819   Spindle  The Array of Microtubules and Associated Molecules That Forms Between Opposite Poles of a Eukaryotic Cell During Mitosis or Meiosis and Serves to Move the Duplicated Chromosomes Apart. 
    5515   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). 
    35064   Methylated Histone Binding  Interacting Selectively and Non Covalently with a Histone Protein in Which a Residue Has Been Modified by Methylation. Histones Are Any of a Group of Water Soluble Proteins Found in Association with the DNA of Plant and Animal Chromosomes. 

  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene spin1, ocr, spin
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-2T

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    9 9q22.1 10927     spindlin 1 SPIN1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs201082729 LS-SNP   dbSNP   A 173 D - > G Beta Ladder 13% (Intermediate) 9 91083449
    rs34794905 LS-SNP   dbSNP   A 221 A - > P Beta Ladder 89% (Exposed) 9 91090064