Entry Database : PDB / ID : 4gdk Structure visualization Downloads & linksTitle Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 ComponentsAutophagy protein 5 Autophagy-related protein 16-1 Ubiquitin-like protein ATG12 DetailsKeywords PROTEIN BINDING / protein-protein conjugate / protein-protein complex / ubiquitin-like protein / autophagy / E3 ligase / ubiquitin-like fold / structural protein / isopeptide bond / Cytoplasm and autophagosomal membranesFunction / homology Function and homology informationFunction Domain/homology Component
otolith development / regulation of autophagosome maturation / positive regulation of viral translation / response to fluoride / C-terminal protein lipidation / regulation of cytokine production involved in immune response / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / negative regulation of dendrite extension ... otolith development / regulation of autophagosome maturation / positive regulation of viral translation / response to fluoride / C-terminal protein lipidation / regulation of cytokine production involved in immune response / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / negative regulation of dendrite extension / vacuole-isolation membrane contact site / phagophore / negative regulation of autophagic cell death / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / cellular response to nitrosative stress / ventricular cardiac muscle cell development / microautophagy / positive regulation of stress granule assembly / glycophagy / regulation of cilium assembly / transferase complex / aggrephagy / dendrite arborization / mucus secretion / mitochondria-associated endoplasmic reticulum membrane contact site / response to fungus / xenophagy / corpus callosum development / protein localization to phagophore assembly site / negative thymic T cell selection / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / cellular response to nitrogen starvation / response to iron(II) ion / positive regulation of mucus secretion / regulation of reactive oxygen species metabolic process / negative regulation of cardiac muscle cell apoptotic process / negative regulation of phagocytosis / axonal transport / negative regulation of type I interferon production / Receptor Mediated Mitophagy / Macroautophagy / chaperone-mediated autophagy / heart contraction / autophagosome membrane / blood vessel remodeling / autophagosome assembly / axoneme / autophagosome maturation / regulation of postsynaptic membrane neurotransmitter receptor levels / postsynaptic modulation of chemical synaptic transmission / mitophagy / membrane-membrane adaptor activity / positive regulation of autophagy / sperm midpiece / cardiac muscle cell apoptotic process / negative regulation of protein ubiquitination / post-translational protein modification / autophagosome / negative regulation of innate immune response / hippocampus development / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / macroautophagy / Schaffer collateral - CA1 synapse / autophagy / protein tag activity / phagocytic vesicle membrane / vasodilation / protein transport / chromatin organization / GTPase binding / defense response to virus / postsynapse / protein ubiquitination / response to xenobiotic stimulus / axon / innate immune response / intracellular membrane-bounded organelle / glutamatergic synapse / protein-containing complex / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : ... Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : / Autophagy protein ATG5, UblB domain / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homologyBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution : 2.7 Å DetailsAuthors Otomo, C. / Metlagel, Z. / Takaesu, G. / Otomo, T. CitationJournal : Nat.Struct.Mol.Biol. / Year : 2013Title : Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy.Authors : Otomo, C. / Metlagel, Z. / Takaesu, G. / Otomo, T. History Deposition Jul 31, 2012 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Dec 5, 2012 Provider : repository / Type : Initial releaseRevision 1.1 Jan 2, 2013 Group : Database referencesRevision 1.2 Jan 16, 2013 Group : Database referencesRevision 1.3 Nov 15, 2017 Group : Refinement description / Category : softwareItem : _software.classification / _software.contact_author ... _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version Revision 1.4 Nov 20, 2024 Group : Data collection / Database references ... Data collection / Database references / Derived calculations / Structure summary Category : chem_comp_atom / chem_comp_bond ... chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site Item : _database_2.pdbx_DOI / _database_2.pdbx_database_accession ... _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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