4GDK

Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000045	biological_process	autophagosome assembly
A	0005737	cellular_component	cytoplasm
B	0000045	biological_process	autophagosome assembly
B	0000422	biological_process	autophagy of mitochondrion
B	0000423	biological_process	mitophagy
B	0001974	biological_process	blood vessel remodeling
B	0002376	biological_process	immune system process
B	0002718	biological_process	regulation of cytokine production involved in immune response
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005776	cellular_component	autophagosome
B	0005829	cellular_component	cytosol
B	0005930	cellular_component	axoneme
B	0006325	biological_process	chromatin organization
B	0006914	biological_process	autophagy
B	0006915	biological_process	apoptotic process
B	0006995	biological_process	cellular response to nitrogen starvation
B	0009267	biological_process	cellular response to starvation
B	0009410	biological_process	response to xenobiotic stimulus
B	0009620	biological_process	response to fungus
B	0010040	biological_process	response to iron(II) ion
B	0010659	biological_process	cardiac muscle cell apoptotic process
B	0010667	biological_process	negative regulation of cardiac muscle cell apoptotic process
B	0016020	cellular_component	membrane
B	0016236	biological_process	macroautophagy
B	0016567	biological_process	protein ubiquitination
B	0019776	molecular_function	Atg8-family ligase activity
B	0019883	biological_process	antigen processing and presentation of endogenous antigen
B	0030424	cellular_component	axon
B	0030670	cellular_component	phagocytic vesicle membrane
B	0031397	biological_process	negative regulation of protein ubiquitination
B	0032480	biological_process	negative regulation of type I interferon production
B	0032991	cellular_component	protein-containing complex
B	0034045	cellular_component	phagophore assembly site membrane
B	0034274	cellular_component	Atg12-Atg5-Atg16 complex
B	0034727	biological_process	piecemeal microautophagy of the nucleus
B	0035973	biological_process	aggrephagy
B	0039689	biological_process	negative stranded viral RNA replication
B	0042311	biological_process	vasodilation
B	0043066	biological_process	negative regulation of apoptotic process
B	0043687	biological_process	post-translational protein modification
B	0044233	cellular_component	mitochondria-associated endoplasmic reticulum membrane contact site
B	0045060	biological_process	negative thymic T cell selection
B	0045087	biological_process	innate immune response
B	0045202	cellular_component	synapse
B	0045824	biological_process	negative regulation of innate immune response
B	0048840	biological_process	otolith development
B	0050687	biological_process	negative regulation of defense response to virus
B	0050765	biological_process	negative regulation of phagocytosis
B	0051279	biological_process	regulation of release of sequestered calcium ion into cytosol
B	0051607	biological_process	defense response to virus
B	0051649	biological_process	establishment of localization in cell
B	0055015	biological_process	ventricular cardiac muscle cell development
B	0060047	biological_process	heart contraction
B	0061684	biological_process	chaperone-mediated autophagy
B	0061908	cellular_component	phagophore
B	0062029	biological_process	positive regulation of stress granule assembly
B	0070254	biological_process	mucus secretion
B	0070257	biological_process	positive regulation of mucus secretion
B	0071500	biological_process	cellular response to nitrosative stress
B	0098685	cellular_component	Schaffer collateral - CA1 synapse
B	0098794	cellular_component	postsynapse
B	0098930	biological_process	axonal transport
B	0098978	cellular_component	glutamatergic synapse
B	0099072	biological_process	regulation of postsynaptic membrane neurotransmitter receptor levels
B	0099170	biological_process	postsynaptic modulation of chemical synaptic transmission
B	1901096	biological_process	regulation of autophagosome maturation
B	1902017	biological_process	regulation of cilium assembly
B	1902617	biological_process	response to fluoride
B	1904093	biological_process	negative regulation of autophagic cell death
B	1904973	biological_process	positive regulation of viral translation
B	1990234	cellular_component	transferase complex
B	2000377	biological_process	regulation of reactive oxygen species metabolic process
B	2000378	biological_process	negative regulation of reactive oxygen species metabolic process
D	0000045	biological_process	autophagosome assembly
D	0005737	cellular_component	cytoplasm
E	0000045	biological_process	autophagosome assembly
E	0000422	biological_process	autophagy of mitochondrion
E	0000423	biological_process	mitophagy
E	0001974	biological_process	blood vessel remodeling
E	0002376	biological_process	immune system process
E	0002718	biological_process	regulation of cytokine production involved in immune response
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005776	cellular_component	autophagosome
E	0005829	cellular_component	cytosol
E	0005930	cellular_component	axoneme
E	0006325	biological_process	chromatin organization
E	0006914	biological_process	autophagy
E	0006915	biological_process	apoptotic process
E	0006995	biological_process	cellular response to nitrogen starvation
E	0009267	biological_process	cellular response to starvation
E	0009410	biological_process	response to xenobiotic stimulus
E	0009620	biological_process	response to fungus
E	0010040	biological_process	response to iron(II) ion
E	0010659	biological_process	cardiac muscle cell apoptotic process
E	0010667	biological_process	negative regulation of cardiac muscle cell apoptotic process
E	0016020	cellular_component	membrane
E	0016236	biological_process	macroautophagy
E	0016567	biological_process	protein ubiquitination
E	0019776	molecular_function	Atg8-family ligase activity
E	0019883	biological_process	antigen processing and presentation of endogenous antigen
E	0030424	cellular_component	axon
E	0030670	cellular_component	phagocytic vesicle membrane
E	0031397	biological_process	negative regulation of protein ubiquitination
E	0032480	biological_process	negative regulation of type I interferon production
E	0032991	cellular_component	protein-containing complex
E	0034045	cellular_component	phagophore assembly site membrane
E	0034274	cellular_component	Atg12-Atg5-Atg16 complex
E	0034727	biological_process	piecemeal microautophagy of the nucleus
E	0035973	biological_process	aggrephagy
E	0039689	biological_process	negative stranded viral RNA replication
E	0042311	biological_process	vasodilation
E	0043066	biological_process	negative regulation of apoptotic process
E	0043687	biological_process	post-translational protein modification
E	0044233	cellular_component	mitochondria-associated endoplasmic reticulum membrane contact site
E	0045060	biological_process	negative thymic T cell selection
E	0045087	biological_process	innate immune response
E	0045202	cellular_component	synapse
E	0045824	biological_process	negative regulation of innate immune response
E	0048840	biological_process	otolith development
E	0050687	biological_process	negative regulation of defense response to virus
E	0050765	biological_process	negative regulation of phagocytosis
E	0051279	biological_process	regulation of release of sequestered calcium ion into cytosol
E	0051607	biological_process	defense response to virus
E	0051649	biological_process	establishment of localization in cell
E	0055015	biological_process	ventricular cardiac muscle cell development
E	0060047	biological_process	heart contraction
E	0061684	biological_process	chaperone-mediated autophagy
E	0061908	cellular_component	phagophore
E	0062029	biological_process	positive regulation of stress granule assembly
E	0070254	biological_process	mucus secretion
E	0070257	biological_process	positive regulation of mucus secretion
E	0071500	biological_process	cellular response to nitrosative stress
E	0098685	cellular_component	Schaffer collateral - CA1 synapse
E	0098794	cellular_component	postsynapse
E	0098930	biological_process	axonal transport
E	0098978	cellular_component	glutamatergic synapse
E	0099072	biological_process	regulation of postsynaptic membrane neurotransmitter receptor levels
E	0099170	biological_process	postsynaptic modulation of chemical synaptic transmission
E	1901096	biological_process	regulation of autophagosome maturation
E	1902017	biological_process	regulation of cilium assembly
E	1902617	biological_process	response to fluoride
E	1904093	biological_process	negative regulation of autophagic cell death
E	1904973	biological_process	positive regulation of viral translation
E	1990234	cellular_component	transferase complex
E	2000377	biological_process	regulation of reactive oxygen species metabolic process
E	2000378	biological_process	negative regulation of reactive oxygen species metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 301

Chain	Residue
B	ALA95
B	PRO97
B	ASN99
B	HOH424
B	HOH437
B	HOH438

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site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA E 301

Chain	Residue
E	HOH407
E	HOH413
E	ALA95
E	PRO97
E	ASN99

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Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:22814378

Chain	Residue	Details
B	MET1
E	MET1
D	GLY140

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site_id	SWS_FT_FI2
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ATG12) => ECO:0000305

Chain	Residue	Details
B	LYS130
E	LYS130

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