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Crystal structure of an Atg7-Atg10 crosslinked complex
Biology and Chemistry Report
4GSK
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN TRANSPORT/LIGASE
    Text Ubiquitin-like protein activation enzyme, Ubiquitin-like protein transfer enzyme, PROTEIN TRANSPORT-LIGASE complex

    Polymeric Molecules

    Chain A,B
    Description Ubiquitin-like modifier-activating enzyme ATG7 
    Fragment UNP residues 1-613 
    Mutation C39S, C195S, C375A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 69628.7 
    Source Method genetically manipulated  
    Entity Name ATG12-activating enzyme E1 ATG7, Autophagy-related protein 7, Cytoplasm to vacuole targeting protein 2 
    Chain Y,Z
    Description Ubiquitin-like-conjugating enzyme ATG10 
    Mutation C26S, C137S 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 20148.0 
    Source Method genetically manipulated  
    Entity Name Autophagy-related protein 10 

    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 ATG7_YEAST D3DLC0     
    Y,Z ATG10_YEAST D6VXW4     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    Y Z  6.3.2      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    422   Mitochondrion Degradation  The Autophagic Process in Which Mitochondria Are Delivered to the Vacuole and Degraded in Response to Changing Cellular Conditions. 
    6501   C Terminal Protein Lipidation  The Covalent Attachment of a Lipid Group to the Carboxy Terminus of a Protein. 
    6810   Transport  The Directed Movement of Substances (such As Macromolecules Small Molecules Ions) Into Out of or Within a Cell or Between Cells or Within a Multicellular Organism by Means of Some Agent Such As a Transporter or Pore. 
    6914   Autophagy  The Process in Which Cells Digest Parts of Their Own Cytoplasm; Allows For Both Recycling of Macromolecular Constituents Under Conditions of Cellular Stress and Remodeling the Intracellular Structure For Cell Differentiation. 
    15031   Protein Transport  The Directed Movement of Proteins Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    16236   Macroautophagy  The Major Inducible Pathway For the General Turnover of Cytoplasmic Constituents in Eukaryotic Cells It Is Also Responsible For the Degradation of Active Cytoplasmic Enzymes and Organelles During Nutrient Starvation. Macroautophagy Involves the Formation of Double Membrane Bounded Autophagosomes Which Enclose the Cytoplasmic Constituent Targeted For Degradation in a Membrane Bounded Structure Which Then Fuse with the Lysosome (or Vacuole) Releasing a Single Membrane Bounded Autophagic Bodies Which Are Then Degraded Within the Lysosome (or Vacuole). Though Once Thought to Be a Purely Non Selective Process It Appears That Some Types of Macroautophagy E.g. Macropexophagy Macromitophagy May Involve Selective Targeting of the Targets to Be Degraded. 
    32258   Cvt Pathway  A Constitutive Biosynthetic Process That Occurs Under Nutrient Rich Conditions in Which Two Resident Vacuolar Hydrolases Aminopeptidase I and Alpha Mannosidase Are Sequestered Into Vesicles; These Vesicles Are Transported to and Then Fuse with the Vacuole. This Pathway Is Mostly Observed in Yeast. 
    32446   Protein Modification by Small Protein Conjugation  A Protein Modification Process in Which One or More Groups of a Small Protein Such As Ubiquitin or a Ubiquitin Like Protein Are Covalently Attached to a Target Protein. 
    34727   Piecemeal Microautophagy of Nucleus  Degradation of a Cell Nucleus by Microautophagy. 
    44805   Late Nucleophagy  A Type of Nucleophagy Distinct From Piecemeal Microautophagy of the Nucleus (pnm) Where the Nuclear Material Is Delivered to the Vacuole/lysosome For Breakdown and Recycling Later Than Observed For Pnm. 
    407   Pre Autophagosomal Structure  A Punctate Structure Localized in the Vicinity of the Vacuole That Is Required For the Formation of Autophagosomes. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    97632   Extrinsic Component of Pre Autophagosomal Structure Membrane  The Component of the Pre Autophagosomal Structure Membrane Consisting of Gene Products and Protein Complexes That Are Loosely Bound to One of Its Surfaces But Not Integrated Into the Hydrophobic Region. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    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). 
    19778   Atg12 Activating Enzyme Activity  Catalysis of the Activation of the Small Ubiquitin Related Modifier Apg12 Through the Formation of an ATP Dependent High Energy Thiolester Bond. 
    19779   Atg8 Activating Enzyme  Catalysis of the Activation of the Small Ubiquitin Related Modifier Apg8 Through the Formation of an ATP Dependent High Energy Thiolester Bond. 
    Chain Y,Z
    GO ID   Ontology GO Term Definition
    422   Mitochondrion Degradation  The Autophagic Process in Which Mitochondria Are Delivered to the Vacuole and Degraded in Response to Changing Cellular Conditions. 
    6464   Cellular Protein Modification Process  The Covalent Alteration of One or More Amino Acids Occurring in Proteins Peptides and Nascent Polypeptides (co Translational Post Translational Modifications) Occurring At the Level of an Individual Cell. Includes the Modification of Charged Trnas That Are Destined to Occur in a Protein (pre Translation Modification). 
    6810   Transport  The Directed Movement of Substances (such As Macromolecules Small Molecules Ions) Into Out of or Within a Cell or Between Cells or Within a Multicellular Organism by Means of Some Agent Such As a Transporter or Pore. 
    6914   Autophagy  The Process in Which Cells Digest Parts of Their Own Cytoplasm; Allows For Both Recycling of Macromolecular Constituents Under Conditions of Cellular Stress and Remodeling the Intracellular Structure For Cell Differentiation. 
    15031   Protein Transport  The Directed Movement of Proteins Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    16236   Macroautophagy  The Major Inducible Pathway For the General Turnover of Cytoplasmic Constituents in Eukaryotic Cells It Is Also Responsible For the Degradation of Active Cytoplasmic Enzymes and Organelles During Nutrient Starvation. Macroautophagy Involves the Formation of Double Membrane Bounded Autophagosomes Which Enclose the Cytoplasmic Constituent Targeted For Degradation in a Membrane Bounded Structure Which Then Fuse with the Lysosome (or Vacuole) Releasing a Single Membrane Bounded Autophagic Bodies Which Are Then Degraded Within the Lysosome (or Vacuole). Though Once Thought to Be a Purely Non Selective Process It Appears That Some Types of Macroautophagy E.g. Macropexophagy Macromitophagy May Involve Selective Targeting of the Targets to Be Degraded. 
    32258   Cvt Pathway  A Constitutive Biosynthetic Process That Occurs Under Nutrient Rich Conditions in Which Two Resident Vacuolar Hydrolases Aminopeptidase I and Alpha Mannosidase Are Sequestered Into Vesicles; These Vesicles Are Transported to and Then Fuse with the Vacuole. This Pathway Is Mostly Observed in Yeast. 
    34727   Piecemeal Microautophagy of Nucleus  Degradation of a Cell Nucleus by Microautophagy. 
    44805   Late Nucleophagy  A Type of Nucleophagy Distinct From Piecemeal Microautophagy of the Nucleus (pnm) Where the Nuclear Material Is Delivered to the Vacuole/lysosome For Breakdown and Recycling Later Than Observed For Pnm. 
    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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    34045   Pre Autophagosomal Structure Membrane  A Cellular Membrane Associated with the Pre Autophagosomal Structure. 
    16874   Ligase Activity  Catalysis of the Joining of Two Substances or Two Groups Within a Single Molecule with the Concomitant Hydrolysis of the Diphosphate Bond in ATP or a Similar Triphosphate. 
    19777   Atg12 Transferase Activity  Catalysis of the Transfer of Ubiquitin From One Protein to Another Via the Reaction X Atg12 + Y > Y Atg12 + X Where Both X Atg12 and Y Atg12 Are Covalent Linkages. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain Y,Z
    Common Name Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene apg10, atg10, yll042c
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3) Ril
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-4T1


    Chain A,B
    Common Name Yeast
    Scientific Name Saccharomyces cerevisiae  
    Strain ATCC 204508 / S288C
    Gene apg7, atg7, cvt2, yhr171w
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3) Gold
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-4T1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    XII - 850684     Atg10p ATG10    
    VIII - 856576     Atg7p ATG7