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Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3
Biology and Chemistry Report
4GY5
  •   Structure Details   Hide

    Structure Keywords

    Keywords Ligase
    Text Histone binding, Ligase

    Polymeric Molecules

    Chain A,B,C,D
    Description E3 ubiquitin-protein ligase UHRF1 
    Fragment Tudor PHD domain, UNP residues 134-366 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 27794.4 
    Source Method genetically manipulated  
    Entity Name UHRF1 
    Chain E,F
    Description Peptide from Histone H3.3 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 1862.2 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D UHRF1_HUMAN Q96T88     
    E,F H33_HUMAN P84243     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D  6.3.2      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 
    Chain E,F
    GO ID   Ontology GO Term Definition
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene uhrf1
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q42.12 3020     H3 histone, family 3A H3F3A    
    17 17q25.1 3021     H3 histone, family 3B (H3.3B) H3F3B    
    19 19p13.3 29128     ubiquitin-like with PHD and ring finger domains 1 UHRF1    

    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
    rs61741143 LS-SNP   dbSNP   A 137 V - > A Turn 47% (Exposed) 19 4930729
    rs200969637 LS-SNP   dbSNP   A 144 R - > Q Beta Ladder 25% (Intermediate) 19 4930750
    rs187926399 LS-SNP   dbSNP   A 196 V - > M Beta Ladder 62% (Exposed) 19 4932769
    rs77416951 LS-SNP   dbSNP   A 216 D - > G 3/10 Helix 54% (Exposed) 19 4932830
    rs17886098 LS-SNP   dbSNP   A 240 D - > H Beta Ladder 17% (Intermediate) 19 4932901
    rs2292148 LS-SNP   dbSNP   A 308 D - > N Coil 19% (Intermediate) 19 4941792