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4NAW

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3

Functional Information from GO Data
ChainGOidnamespacecontents
A0000045biological_processautophagosome assembly
A0005737cellular_componentcytoplasm
B0000045biological_processautophagosome assembly
B0000422biological_processautophagy of mitochondrion
B0000423biological_processmitophagy
B0001974biological_processblood vessel remodeling
B0002376biological_processimmune system process
B0002718biological_processregulation of cytokine production involved in immune response
B0005515molecular_functionprotein binding
B0005737cellular_componentcytoplasm
B0005776cellular_componentautophagosome
B0005829cellular_componentcytosol
B0005930cellular_componentaxoneme
B0006325biological_processchromatin organization
B0006914biological_processautophagy
B0006915biological_processapoptotic process
B0006995biological_processcellular response to nitrogen starvation
B0009267biological_processcellular response to starvation
B0009410biological_processresponse to xenobiotic stimulus
B0009620biological_processresponse to fungus
B0010040biological_processresponse to iron(II) ion
B0010659biological_processcardiac muscle cell apoptotic process
B0010667biological_processnegative regulation of cardiac muscle cell apoptotic process
B0016020cellular_componentmembrane
B0016236biological_processmacroautophagy
B0016567biological_processprotein ubiquitination
B0019776molecular_functionAtg8-family ligase activity
B0019883biological_processantigen processing and presentation of endogenous antigen
B0030424cellular_componentaxon
B0030670cellular_componentphagocytic vesicle membrane
B0031397biological_processnegative regulation of protein ubiquitination
B0032480biological_processnegative regulation of type I interferon production
B0032991cellular_componentprotein-containing complex
B0034045cellular_componentphagophore assembly site membrane
B0034274cellular_componentAtg12-Atg5-Atg16 complex
B0034727biological_processpiecemeal microautophagy of the nucleus
B0035973biological_processaggrephagy
B0039689biological_processnegative stranded viral RNA replication
B0042311biological_processvasodilation
B0043066biological_processnegative regulation of apoptotic process
B0043687biological_processpost-translational protein modification
B0044233cellular_componentmitochondria-associated endoplasmic reticulum membrane contact site
B0045060biological_processnegative thymic T cell selection
B0045824biological_processnegative regulation of innate immune response
B0048840biological_processotolith development
B0050687biological_processnegative regulation of defense response to virus
B0050765biological_processnegative regulation of phagocytosis
B0051279biological_processregulation of release of sequestered calcium ion into cytosol
B0051649biological_processestablishment of localization in cell
B0055015biological_processventricular cardiac muscle cell development
B0060047biological_processheart contraction
B0061684biological_processchaperone-mediated autophagy
B0061908cellular_componentphagophore
B0062029biological_processpositive regulation of stress granule assembly
B0070254biological_processmucus secretion
B0070257biological_processpositive regulation of mucus secretion
B0071500biological_processcellular response to nitrosative stress
B1901096biological_processregulation of autophagosome maturation
B1902017biological_processregulation of cilium assembly
B1902617biological_processresponse to fluoride
B1904093biological_processnegative regulation of autophagic cell death
B1904973biological_processpositive regulation of viral translation
B1990234cellular_componenttransferase complex
B2000377biological_processregulation of reactive oxygen species metabolic process
B2000378biological_processnegative regulation of reactive oxygen species metabolic process
E0000045biological_processautophagosome assembly
E0005737cellular_componentcytoplasm
F0000045biological_processautophagosome assembly
F0000422biological_processautophagy of mitochondrion
F0000423biological_processmitophagy
F0001974biological_processblood vessel remodeling
F0002376biological_processimmune system process
F0002718biological_processregulation of cytokine production involved in immune response
F0005515molecular_functionprotein binding
F0005737cellular_componentcytoplasm
F0005776cellular_componentautophagosome
F0005829cellular_componentcytosol
F0005930cellular_componentaxoneme
F0006325biological_processchromatin organization
F0006914biological_processautophagy
F0006915biological_processapoptotic process
F0006995biological_processcellular response to nitrogen starvation
F0009267biological_processcellular response to starvation
F0009410biological_processresponse to xenobiotic stimulus
F0009620biological_processresponse to fungus
F0010040biological_processresponse to iron(II) ion
F0010659biological_processcardiac muscle cell apoptotic process
F0010667biological_processnegative regulation of cardiac muscle cell apoptotic process
F0016020cellular_componentmembrane
F0016236biological_processmacroautophagy
F0016567biological_processprotein ubiquitination
F0019776molecular_functionAtg8-family ligase activity
F0019883biological_processantigen processing and presentation of endogenous antigen
F0030424cellular_componentaxon
F0030670cellular_componentphagocytic vesicle membrane
F0031397biological_processnegative regulation of protein ubiquitination
F0032480biological_processnegative regulation of type I interferon production
F0032991cellular_componentprotein-containing complex
F0034045cellular_componentphagophore assembly site membrane
F0034274cellular_componentAtg12-Atg5-Atg16 complex
F0034727biological_processpiecemeal microautophagy of the nucleus
F0035973biological_processaggrephagy
F0039689biological_processnegative stranded viral RNA replication
F0042311biological_processvasodilation
F0043066biological_processnegative regulation of apoptotic process
F0043687biological_processpost-translational protein modification
F0044233cellular_componentmitochondria-associated endoplasmic reticulum membrane contact site
F0045060biological_processnegative thymic T cell selection
F0045824biological_processnegative regulation of innate immune response
F0048840biological_processotolith development
F0050687biological_processnegative regulation of defense response to virus
F0050765biological_processnegative regulation of phagocytosis
F0051279biological_processregulation of release of sequestered calcium ion into cytosol
F0051649biological_processestablishment of localization in cell
F0055015biological_processventricular cardiac muscle cell development
F0060047biological_processheart contraction
F0061684biological_processchaperone-mediated autophagy
F0061908cellular_componentphagophore
F0062029biological_processpositive regulation of stress granule assembly
F0070254biological_processmucus secretion
F0070257biological_processpositive regulation of mucus secretion
F0071500biological_processcellular response to nitrosative stress
F1901096biological_processregulation of autophagosome maturation
F1902017biological_processregulation of cilium assembly
F1902617biological_processresponse to fluoride
F1904093biological_processnegative regulation of autophagic cell death
F1904973biological_processpositive regulation of viral translation
F1990234cellular_componenttransferase complex
F2000377biological_processregulation of reactive oxygen species metabolic process
F2000378biological_processnegative regulation of reactive oxygen species metabolic process
I0000045biological_processautophagosome assembly
I0005737cellular_componentcytoplasm
J0000045biological_processautophagosome assembly
J0000422biological_processautophagy of mitochondrion
J0000423biological_processmitophagy
J0001974biological_processblood vessel remodeling
J0002376biological_processimmune system process
J0002718biological_processregulation of cytokine production involved in immune response
J0005515molecular_functionprotein binding
J0005737cellular_componentcytoplasm
J0005776cellular_componentautophagosome
J0005829cellular_componentcytosol
J0005930cellular_componentaxoneme
J0006325biological_processchromatin organization
J0006914biological_processautophagy
J0006915biological_processapoptotic process
J0006995biological_processcellular response to nitrogen starvation
J0009267biological_processcellular response to starvation
J0009410biological_processresponse to xenobiotic stimulus
J0009620biological_processresponse to fungus
J0010040biological_processresponse to iron(II) ion
J0010659biological_processcardiac muscle cell apoptotic process
J0010667biological_processnegative regulation of cardiac muscle cell apoptotic process
J0016020cellular_componentmembrane
J0016236biological_processmacroautophagy
J0016567biological_processprotein ubiquitination
J0019776molecular_functionAtg8-family ligase activity
J0019883biological_processantigen processing and presentation of endogenous antigen
J0030424cellular_componentaxon
J0030670cellular_componentphagocytic vesicle membrane
J0031397biological_processnegative regulation of protein ubiquitination
J0032480biological_processnegative regulation of type I interferon production
J0032991cellular_componentprotein-containing complex
J0034045cellular_componentphagophore assembly site membrane
J0034274cellular_componentAtg12-Atg5-Atg16 complex
J0034727biological_processpiecemeal microautophagy of the nucleus
J0035973biological_processaggrephagy
J0039689biological_processnegative stranded viral RNA replication
J0042311biological_processvasodilation
J0043066biological_processnegative regulation of apoptotic process
J0043687biological_processpost-translational protein modification
J0044233cellular_componentmitochondria-associated endoplasmic reticulum membrane contact site
J0045060biological_processnegative thymic T cell selection
J0045824biological_processnegative regulation of innate immune response
J0048840biological_processotolith development
J0050687biological_processnegative regulation of defense response to virus
J0050765biological_processnegative regulation of phagocytosis
J0051279biological_processregulation of release of sequestered calcium ion into cytosol
J0051649biological_processestablishment of localization in cell
J0055015biological_processventricular cardiac muscle cell development
J0060047biological_processheart contraction
J0061684biological_processchaperone-mediated autophagy
J0061908cellular_componentphagophore
J0062029biological_processpositive regulation of stress granule assembly
J0070254biological_processmucus secretion
J0070257biological_processpositive regulation of mucus secretion
J0071500biological_processcellular response to nitrosative stress
J1901096biological_processregulation of autophagosome maturation
J1902017biological_processregulation of cilium assembly
J1902617biological_processresponse to fluoride
J1904093biological_processnegative regulation of autophagic cell death
J1904973biological_processpositive regulation of viral translation
J1990234cellular_componenttransferase complex
J2000377biological_processregulation of reactive oxygen species metabolic process
J2000378biological_processnegative regulation of reactive oxygen species metabolic process
M0000045biological_processautophagosome assembly
M0005737cellular_componentcytoplasm
N0000045biological_processautophagosome assembly
N0000422biological_processautophagy of mitochondrion
N0000423biological_processmitophagy
N0001974biological_processblood vessel remodeling
N0002376biological_processimmune system process
N0002718biological_processregulation of cytokine production involved in immune response
N0005515molecular_functionprotein binding
N0005737cellular_componentcytoplasm
N0005776cellular_componentautophagosome
N0005829cellular_componentcytosol
N0005930cellular_componentaxoneme
N0006325biological_processchromatin organization
N0006914biological_processautophagy
N0006915biological_processapoptotic process
N0006995biological_processcellular response to nitrogen starvation
N0009267biological_processcellular response to starvation
N0009410biological_processresponse to xenobiotic stimulus
N0009620biological_processresponse to fungus
N0010040biological_processresponse to iron(II) ion
N0010659biological_processcardiac muscle cell apoptotic process
N0010667biological_processnegative regulation of cardiac muscle cell apoptotic process
N0016020cellular_componentmembrane
N0016236biological_processmacroautophagy
N0016567biological_processprotein ubiquitination
N0019776molecular_functionAtg8-family ligase activity
N0019883biological_processantigen processing and presentation of endogenous antigen
N0030424cellular_componentaxon
N0030670cellular_componentphagocytic vesicle membrane
N0031397biological_processnegative regulation of protein ubiquitination
N0032480biological_processnegative regulation of type I interferon production
N0032991cellular_componentprotein-containing complex
N0034045cellular_componentphagophore assembly site membrane
N0034274cellular_componentAtg12-Atg5-Atg16 complex
N0034727biological_processpiecemeal microautophagy of the nucleus
N0035973biological_processaggrephagy
N0039689biological_processnegative stranded viral RNA replication
N0042311biological_processvasodilation
N0043066biological_processnegative regulation of apoptotic process
N0043687biological_processpost-translational protein modification
N0044233cellular_componentmitochondria-associated endoplasmic reticulum membrane contact site
N0045060biological_processnegative thymic T cell selection
N0045824biological_processnegative regulation of innate immune response
N0048840biological_processotolith development
N0050687biological_processnegative regulation of defense response to virus
N0050765biological_processnegative regulation of phagocytosis
N0051279biological_processregulation of release of sequestered calcium ion into cytosol
N0051649biological_processestablishment of localization in cell
N0055015biological_processventricular cardiac muscle cell development
N0060047biological_processheart contraction
N0061684biological_processchaperone-mediated autophagy
N0061908cellular_componentphagophore
N0062029biological_processpositive regulation of stress granule assembly
N0070254biological_processmucus secretion
N0070257biological_processpositive regulation of mucus secretion
N0071500biological_processcellular response to nitrosative stress
N1901096biological_processregulation of autophagosome maturation
N1902017biological_processregulation of cilium assembly
N1902617biological_processresponse to fluoride
N1904093biological_processnegative regulation of autophagic cell death
N1904973biological_processpositive regulation of viral translation
N1990234cellular_componenttransferase complex
N2000377biological_processregulation of reactive oxygen species metabolic process
N2000378biological_processnegative regulation of reactive oxygen species metabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 B 301
ChainResidue
BARG183
BARG204
FALA207
FALA208
FASP209

site_idAC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 B 302
ChainResidue
BHOH414
BHOH470
BHOH516
JARG30
BARG161
BPHE162
BASP163
BGLN164

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA B 303
ChainResidue
BALA95
BPRO97
BASN99
BHOH405
BHOH413
JHOH410

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 F 301
ChainResidue
CGLN30
FSER94
FALA95
FHOH407

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 F 302
ChainResidue
FLYS138
FARG183
FARG204

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA F 303
ChainResidue
FALA95
FPRO97
FASN99
FHOH401
FHOH407
FHOH412

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 J 301
ChainResidue
BSER94
BALA95
GGLN30
JARG161
JHOH410

site_idAC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 J 302
ChainResidue
JSER94
JALA95
OGLN30

site_idAC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 J 303
ChainResidue
JLYS138
JARG183
JARG204

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 J 304
ChainResidue
JARG161
JPHE162
JASP163
JGLN164
JHOH509

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NA J 305
ChainResidue
JALA95
JPRO97
JASN99
JHOH514

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 N 301
ChainResidue
BSER117
BLYS118
NLYS51
NHOH427
NHOH428
NHOH450

site_idBC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 N 302
ChainResidue
NARG183
NARG204

site_idBC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 N 303
ChainResidue
NARG161
NASP163
NGLN164
NHOH424

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NA N 304
ChainResidue
NALA95
NPRO97
NASN99
NHOH405

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-130 in ATG5) => ECO:0000269|PubMed:23202584
ChainResidueDetails
AGLY140
HASP169
EGLY140
PASP169
IGLY140
MGLY140

site_idSWS_FT_FI2
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ATG12) => ECO:0000305
ChainResidueDetails
BLYS130
FLYS130
JLYS130
NLYS130

222415

PDB entries from 2024-07-10

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