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Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin
Biology and Chemistry Report
3VHT
  •   Structure Details   Hide

    Structure Keywords

    Keywords FLUORESCENT PROTEIN/PROTEIN BINDING
    Text GREEN FLUORESCENT PROTEIN, FUSION PROTEIN, ZINC FINGER, UBIQUITIN-BINDING DOMAIN, FLUORESCENT PROTEIN-PROTEIN BINDING complex

    Polymeric Molecules

    Chain A
    Description Green fluorescent protein 
    Fragment GFP domain 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 26306.8 
    Source Method genetically manipulated  
    Chain B
    Description Green fluorescent protein, ATPase WRNIP1 
    Fragment GFP-Wrnip1 UBZ domain 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 30543.8 
    Source Method genetically manipulated  
    Entity Name Werner helicase-interacting protein 1 
    Chain C
    Description Ubiquitin 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 8576.9 
    Source Method natural source  

    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 GFP_AEQVI P42212     
    B WRIP1_HUMAN Q96S55     
    C E9Q9J0 E9Q9J0     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.6.1.3      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6091   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. 
    8218   Bioluminescence  The Production of Light by Certain Enzyme Catalyzed Reactions in Cells. 
    18298   Protein Chromophore Linkage  The Covalent or Noncovalent Attachment of a Chromophore to a Protein. 
    5575   Cellular_component  The Part of a Cell or Its Extracellular Environment in Which a Gene Product Is Located. a Gene Product May Be Located in One or More Parts of a Cell and Its Location May Be As Specific As a Particular Macromolecular Complex That Is a Stable Persistent Association of Macromolecules That Function Together. 
    3674   Molecular_function  Elemental Activities Such As Catalysis or Binding Describing the Actions of a Gene Product At the Molecular Level. a Given Gene Product May Exhibit One or More Molecular Functions. 
    Chain B
    GO ID   Ontology GO Term Definition
    6091   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. 
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    8218   Bioluminescence  The Production of Light by Certain Enzyme Catalyzed Reactions in Cells. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 


     
  •   Gene Details   Hide

    Natural Source

    Chain C
    Common Name Mouse
    Scientific Name Mus musculus  

    Genetic Source

    Chain B
    Common Name Jellyfish Human
    Scientific Name Aequorea victoria, homo sapiens  
    Gene gfp, whip, wrnip1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET28


    Chain A
    Common Name Jellyfish
    Scientific Name Aequorea victoria  
    Gene gfp
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET28


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6p25.2 56897     Werner helicase interacting protein 1 WRNIP1    
    11 11 B2|11 38.46 cM 22187     ubiquitin B UBB    

    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
    rs146408874 LS-SNP   dbSNP   B 237 S - > P Coil 81% (Exposed) 6 2765893
    rs200233974 LS-SNP   dbSNP   B 239 L - > V Turn 23% (Intermediate) 6 2765899