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Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1
Biology and Chemistry Report
4GDK
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN BINDING
    Text protein-protein conjugate, protein-protein complex, ubiquitin-like protein, autophagy, E3 ligase, ubiquitin-like fold, structural protein, isopeptide bond, Cytoplasm and autophagosomal membranes, PROTEIN BINDING

    Polymeric Molecules

    Chain A,D
    Description Ubiquitin-like protein ATG12 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 10282.1 
    Source Method genetically manipulated  
    Entity Name Autophagy-related protein 12, APG12-like 
    Chain B,E
    Description Autophagy protein 5 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 32489.5 
    Source Method genetically manipulated  
    Entity Name APG5-like, Apoptosis-specific protein 
    Chain C,F
    Description Autophagy-related protein 16-1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 4657.5 
    Source Method genetically manipulated  
    Entity Name APG16-like 1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    NA  SODIUM ION  Na   22.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,D ATG12_HUMAN O94817     
    B,E ATG5_HUMAN O60875     
    C,F A16L1_HUMAN A3EXK9     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,D
    GO ID   Ontology GO Term Definition
    45   Autophagic Vacuole Assembly  The Formation of a Double Membrane Bounded Structure the Autophagosome That Occurs When a Specialized Membrane Sac Called the Isolation Membrane Starts to Enclose a Portion of the Cytoplasm. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    Chain B,E
    GO ID   Ontology GO Term Definition
    45   Autophagic Vacuole Assembly  The Formation of a Double Membrane Bounded Structure the Autophagosome That Occurs When a Specialized Membrane Sac Called the Isolation Membrane Starts to Enclose a Portion of the Cytoplasm. 
    422   Mitochondrion Degradation  The Autophagic Process in Which Mitochondria Are Delivered to the Vacuole and Degraded in Response to Changing Cellular Conditions. 
    1974   Blood Vessel Remodeling  The Reorganization or Renovation of Existing Blood Vessels. 
    2376   Immune System Process  Any Process Involved in the Development or Functioning of the Immune System an Organismal System For Calibrated Responses to Potential Internal or Invasive Threats. 
    2739   Regulation of Cytokine Secretion Involved in Immune Response  Any Process That Modulates the Frequency Rate or Extent of Cytokine Secretion Contributing to an Immune Response. 
    6501   C Terminal Protein Lipidation  The Covalent Attachment of a Lipid Group to the Carboxy Terminus of a Protein. 
    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. 
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    6995   Cellular Response to Nitrogen Starvation  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 Deprivation of Nitrogen. 
    9620   Response to Fungus  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus From a Fungus. 
    31397   Negative Regulation of Protein Ubiquitination  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Addition of Ubiquitin Groups to a Protein. 
    32480   Negative Regulation of Type I Interferon Production  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Type I Interferon Production. Type I Interferons Include the Interferon Alpha Beta Delta Episilon Zeta Kappa Tau and Omega Gene Families. 
    39689   Negative Stranded Viral RNA Replication  A Viral Genome Replication Process Where the Template Genome Is Negative Stranded Single Stranded RNA (( )ssrna). 
    42311   Vasodilation  An Increase in the Internal Diameter of Blood Vessels Especially Arterioles or Capillaries Usually Resulting in a Decrease in Blood Pressure. 
    42493   Response to Drug  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Drug Stimulus. a Drug Is a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    43066   Negative Regulation of Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cell Death by Apoptotic Process. 
    43687   Post Translational Protein Modification  The Process of Covalently Altering One or More Amino Acids in a Protein After the Protein Has Been Completely Translated and Released From the Ribosome. 
    44804   Nucleophagy  A Selective Form of Autophagy by Which Damaged or Non Essential Parts of the Nucleus or Even an Entire Nucleus Is Degraded. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    48840   Otolith Development  The Process Whose Specific Outcome Is the Progression of the Otolith Over Time From Its Formation to the Mature Structure. 
    55015   Ventricular Cardiac Muscle Cell Development  The Process Whose Specific Outcome Is the Progression of a Ventricular Cardiac Muscle Cell Over Time From Its Formation to the Mature State. Cardiac Muscle Cells Are Striated Muscle Cells That Are Responsible For Heart Contraction. the Ventricle Is the Part of the Heart That Pumps Blood Out of the Organ. 
    60047   Heart Contraction  The Multicellular Organismal Process in Which the Heart Decreases in Volume in a Characteristic Way to Propel Blood Through the Body. 
    1902017   Regulation of Cilium Assembly  Any Process That Modulates the Frequency Rate or Extent of Cilium Assembly. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5776   Autophagic Vacuole  A Double Membrane Bounded Compartment in Which Endogenous Cellular Material Is Sequestered; Known As Autophagosome in Yeast. 
    5930   Axoneme  The Bundle of Microtubules and Associated Proteins That Forms the Core of Cilia (also Called Flagella) in Eukaryotic Cells and Is Responsible For Their Movements. 
    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. 
    34274   Atg12 Atg5 Atg16 Complex  A Protein Complex Required For the Expansion of the Autophagosomal Membrane. in Budding Yeast This Complex Consists of Atg12p Atg5p and Atg16p. 
    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). 
    19776   Atg8 Ligase Activity  Catalysis of the Covalent Attachment of the Ubiquitin Like Protein Atg8 to Substrate Molecules; Phosphatidylethanolamine Is a Known Substrate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain C,F
    Common Name Human
    Scientific Name Homo sapiens  
    Gene apg16l, atg16l1, unq9393/pro34307
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET


    Chain B,E
    Common Name Human
    Scientific Name Homo sapiens  
    Gene apg5l, asp, atg5
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pACYC Duet-1


    Chain A,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene apg12, apg12l, atg12
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pACYC Duet-1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2q37.1 55054     autophagy related 16-like 1 (S. cerevisiae) ATG16L1    
    5 5q21-q22 9140     autophagy related 12 ATG12    
    6 6q21 9474     autophagy related 5 ATG5    

    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
    rs143219534 LS-SNP   dbSNP   A 89 K - > R Helix 10% (Intermediate) 5 115173359
    rs189664184 LS-SNP   dbSNP   A 132 H - > R Beta Ladder 9% (Intermediate) 5 115167529
    rs77859116 LS-SNP   dbSNP   B 65 I - > V Coil 24% (Intermediate) 6 106756282
    rs140900064 LS-SNP   dbSNP   B 87 F - > S Helix 1% (Buried) 6 106740958
    rs115576116 LS-SNP   dbSNP   B 95 A - > D Coil 25% (Intermediate) 6 106740934 NA
    rs147641218 LS-SNP   dbSNP   B 121 I - > V Helix 0% (Buried) 6 106727653
    rs34793250 LS-SNP   dbSNP   B 129 M - > V Helix 1% (Buried) 6 106727629