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3J2T

An improved model of the human apoptosome

Replaces:  3IZAReplaces:  3IYT
Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0001666biological_processresponse to hypoxia
A0001822biological_processkidney development
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005576cellular_componentextracellular region
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006915biological_processapoptotic process
A0007399biological_processnervous system development
A0007584biological_processresponse to nutrient
A0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
A0010659biological_processcardiac muscle cell apoptotic process
A0030154biological_processcell differentiation
A0031072molecular_functionheat shock protein binding
A0032991cellular_componentprotein-containing complex
A0034774cellular_componentsecretory granule lumen
A0042802molecular_functionidentical protein binding
A0042981biological_processregulation of apoptotic process
A0043065biological_processpositive regulation of apoptotic process
A0043293cellular_componentapoptosome
A0043531molecular_functionADP binding
A0048731biological_processsystem development
A0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
A0070062cellular_componentextracellular exosome
A0071560biological_processcellular response to transforming growth factor beta stimulus
A0072432biological_processresponse to G1 DNA damage checkpoint signaling
A0097190biological_processapoptotic signaling pathway
A0097193biological_processintrinsic apoptotic signaling pathway
A0140608molecular_functioncysteine-type endopeptidase activator activity
A1904813cellular_componentficolin-1-rich granule lumen
B0000166molecular_functionnucleotide binding
B0001666biological_processresponse to hypoxia
B0001822biological_processkidney development
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005576cellular_componentextracellular region
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006915biological_processapoptotic process
B0007399biological_processnervous system development
B0007584biological_processresponse to nutrient
B0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
B0010659biological_processcardiac muscle cell apoptotic process
B0030154biological_processcell differentiation
B0031072molecular_functionheat shock protein binding
B0032991cellular_componentprotein-containing complex
B0034774cellular_componentsecretory granule lumen
B0042802molecular_functionidentical protein binding
B0042981biological_processregulation of apoptotic process
B0043065biological_processpositive regulation of apoptotic process
B0043293cellular_componentapoptosome
B0043531molecular_functionADP binding
B0048731biological_processsystem development
B0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
B0070062cellular_componentextracellular exosome
B0071560biological_processcellular response to transforming growth factor beta stimulus
B0072432biological_processresponse to G1 DNA damage checkpoint signaling
B0097190biological_processapoptotic signaling pathway
B0097193biological_processintrinsic apoptotic signaling pathway
B0140608molecular_functioncysteine-type endopeptidase activator activity
B1904813cellular_componentficolin-1-rich granule lumen
C0000166molecular_functionnucleotide binding
C0001666biological_processresponse to hypoxia
C0001822biological_processkidney development
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005576cellular_componentextracellular region
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006915biological_processapoptotic process
C0007399biological_processnervous system development
C0007584biological_processresponse to nutrient
C0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
C0010659biological_processcardiac muscle cell apoptotic process
C0030154biological_processcell differentiation
C0031072molecular_functionheat shock protein binding
C0032991cellular_componentprotein-containing complex
C0034774cellular_componentsecretory granule lumen
C0042802molecular_functionidentical protein binding
C0042981biological_processregulation of apoptotic process
C0043065biological_processpositive regulation of apoptotic process
C0043293cellular_componentapoptosome
C0043531molecular_functionADP binding
C0048731biological_processsystem development
C0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
C0070062cellular_componentextracellular exosome
C0071560biological_processcellular response to transforming growth factor beta stimulus
C0072432biological_processresponse to G1 DNA damage checkpoint signaling
C0097190biological_processapoptotic signaling pathway
C0097193biological_processintrinsic apoptotic signaling pathway
C0140608molecular_functioncysteine-type endopeptidase activator activity
C1904813cellular_componentficolin-1-rich granule lumen
D0000166molecular_functionnucleotide binding
D0001666biological_processresponse to hypoxia
D0001822biological_processkidney development
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005576cellular_componentextracellular region
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006915biological_processapoptotic process
D0007399biological_processnervous system development
D0007584biological_processresponse to nutrient
D0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
D0010659biological_processcardiac muscle cell apoptotic process
D0030154biological_processcell differentiation
D0031072molecular_functionheat shock protein binding
D0032991cellular_componentprotein-containing complex
D0034774cellular_componentsecretory granule lumen
D0042802molecular_functionidentical protein binding
D0042981biological_processregulation of apoptotic process
D0043065biological_processpositive regulation of apoptotic process
D0043293cellular_componentapoptosome
D0043531molecular_functionADP binding
D0048731biological_processsystem development
D0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
D0070062cellular_componentextracellular exosome
D0071560biological_processcellular response to transforming growth factor beta stimulus
D0072432biological_processresponse to G1 DNA damage checkpoint signaling
D0097190biological_processapoptotic signaling pathway
D0097193biological_processintrinsic apoptotic signaling pathway
D0140608molecular_functioncysteine-type endopeptidase activator activity
D1904813cellular_componentficolin-1-rich granule lumen
E0000166molecular_functionnucleotide binding
E0001666biological_processresponse to hypoxia
E0001822biological_processkidney development
E0005515molecular_functionprotein binding
E0005524molecular_functionATP binding
E0005576cellular_componentextracellular region
E0005634cellular_componentnucleus
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006915biological_processapoptotic process
E0007399biological_processnervous system development
E0007584biological_processresponse to nutrient
E0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
E0010659biological_processcardiac muscle cell apoptotic process
E0030154biological_processcell differentiation
E0031072molecular_functionheat shock protein binding
E0032991cellular_componentprotein-containing complex
E0034774cellular_componentsecretory granule lumen
E0042802molecular_functionidentical protein binding
E0042981biological_processregulation of apoptotic process
E0043065biological_processpositive regulation of apoptotic process
E0043293cellular_componentapoptosome
E0043531molecular_functionADP binding
E0048731biological_processsystem development
E0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
E0070062cellular_componentextracellular exosome
E0071560biological_processcellular response to transforming growth factor beta stimulus
E0072432biological_processresponse to G1 DNA damage checkpoint signaling
E0097190biological_processapoptotic signaling pathway
E0097193biological_processintrinsic apoptotic signaling pathway
E0140608molecular_functioncysteine-type endopeptidase activator activity
E1904813cellular_componentficolin-1-rich granule lumen
F0000166molecular_functionnucleotide binding
F0001666biological_processresponse to hypoxia
F0001822biological_processkidney development
F0005515molecular_functionprotein binding
F0005524molecular_functionATP binding
F0005576cellular_componentextracellular region
F0005634cellular_componentnucleus
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0006915biological_processapoptotic process
F0007399biological_processnervous system development
F0007584biological_processresponse to nutrient
F0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
F0010659biological_processcardiac muscle cell apoptotic process
F0030154biological_processcell differentiation
F0031072molecular_functionheat shock protein binding
F0032991cellular_componentprotein-containing complex
F0034774cellular_componentsecretory granule lumen
F0042802molecular_functionidentical protein binding
F0042981biological_processregulation of apoptotic process
F0043065biological_processpositive regulation of apoptotic process
F0043293cellular_componentapoptosome
F0043531molecular_functionADP binding
F0048731biological_processsystem development
F0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
F0070062cellular_componentextracellular exosome
F0071560biological_processcellular response to transforming growth factor beta stimulus
F0072432biological_processresponse to G1 DNA damage checkpoint signaling
F0097190biological_processapoptotic signaling pathway
F0097193biological_processintrinsic apoptotic signaling pathway
F0140608molecular_functioncysteine-type endopeptidase activator activity
F1904813cellular_componentficolin-1-rich granule lumen
G0000166molecular_functionnucleotide binding
G0001666biological_processresponse to hypoxia
G0001822biological_processkidney development
G0005515molecular_functionprotein binding
G0005524molecular_functionATP binding
G0005576cellular_componentextracellular region
G0005634cellular_componentnucleus
G0005737cellular_componentcytoplasm
G0005829cellular_componentcytosol
G0006915biological_processapoptotic process
G0007399biological_processnervous system development
G0007584biological_processresponse to nutrient
G0008656molecular_functioncysteine-type endopeptidase activator activity involved in apoptotic process
G0010659biological_processcardiac muscle cell apoptotic process
G0030154biological_processcell differentiation
G0031072molecular_functionheat shock protein binding
G0032991cellular_componentprotein-containing complex
G0034774cellular_componentsecretory granule lumen
G0042802molecular_functionidentical protein binding
G0042981biological_processregulation of apoptotic process
G0043065biological_processpositive regulation of apoptotic process
G0043293cellular_componentapoptosome
G0043531molecular_functionADP binding
G0048731biological_processsystem development
G0070059biological_processintrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
G0070062cellular_componentextracellular exosome
G0071560biological_processcellular response to transforming growth factor beta stimulus
G0072432biological_processresponse to G1 DNA damage checkpoint signaling
G0097190biological_processapoptotic signaling pathway
G0097193biological_processintrinsic apoptotic signaling pathway
G0140608molecular_functioncysteine-type endopeptidase activator activity
G1904813cellular_componentficolin-1-rich granule lumen
H0005758cellular_componentmitochondrial intermembrane space
H0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
H0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
H0006915biological_processapoptotic process
H0009055molecular_functionelectron transfer activity
H0020037molecular_functionheme binding
H0022904biological_processrespiratory electron transport chain
H0046872molecular_functionmetal ion binding
I0005758cellular_componentmitochondrial intermembrane space
I0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
I0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
I0006915biological_processapoptotic process
I0009055molecular_functionelectron transfer activity
I0020037molecular_functionheme binding
I0022904biological_processrespiratory electron transport chain
I0046872molecular_functionmetal ion binding
J0005758cellular_componentmitochondrial intermembrane space
J0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
J0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
J0006915biological_processapoptotic process
J0009055molecular_functionelectron transfer activity
J0020037molecular_functionheme binding
J0022904biological_processrespiratory electron transport chain
J0046872molecular_functionmetal ion binding
K0005758cellular_componentmitochondrial intermembrane space
K0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
K0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
K0006915biological_processapoptotic process
K0009055molecular_functionelectron transfer activity
K0020037molecular_functionheme binding
K0022904biological_processrespiratory electron transport chain
K0046872molecular_functionmetal ion binding
L0005758cellular_componentmitochondrial intermembrane space
L0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
L0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
L0006915biological_processapoptotic process
L0009055molecular_functionelectron transfer activity
L0020037molecular_functionheme binding
L0022904biological_processrespiratory electron transport chain
L0046872molecular_functionmetal ion binding
M0005758cellular_componentmitochondrial intermembrane space
M0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
M0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
M0006915biological_processapoptotic process
M0009055molecular_functionelectron transfer activity
M0020037molecular_functionheme binding
M0022904biological_processrespiratory electron transport chain
M0046872molecular_functionmetal ion binding
N0005758cellular_componentmitochondrial intermembrane space
N0006122biological_processmitochondrial electron transport, ubiquinol to cytochrome c
N0006123biological_processmitochondrial electron transport, cytochrome c to oxygen
N0006915biological_processapoptotic process
N0009055molecular_functionelectron transfer activity
N0020037molecular_functionheme binding
N0022904biological_processrespiratory electron transport chain
N0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP A 1301
ChainResidue
AVAL125
ASER161
AVAL162
AILE294
APRO321
ALEU322
ASER325
APHE126
AVAL127
AARG129
AMET155
AGLY157
ACYS158
AGLY159
ALYS160

site_idAC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP B 1301
ChainResidue
BVAL125
BPHE126
BVAL127
BARG129
BMET155
BGLY157
BCYS158
BGLY159
BLYS160
BSER161
BVAL162
BILE294
BPRO321
BLEU322
BSER325

site_idAC3
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP C 1301
ChainResidue
CVAL125
CPHE126
CVAL127
CARG129
CMET155
CGLY157
CCYS158
CGLY159
CLYS160
CSER161
CVAL162
CILE294
CPRO321
CLEU322
CSER325

site_idAC4
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP D 1301
ChainResidue
DVAL125
DPHE126
DVAL127
DARG129
DMET155
DGLY157
DCYS158
DGLY159
DLYS160
DSER161
DVAL162
DILE294
DPRO321
DLEU322
DSER325

site_idAC5
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP E 1301
ChainResidue
EVAL125
EPHE126
EVAL127
EARG129
EMET155
EGLY157
ECYS158
EGLY159
ELYS160
ESER161
EVAL162
EILE294
EPRO321
ELEU322
ESER325

site_idAC6
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP F 1301
ChainResidue
FVAL125
FPHE126
FVAL127
FARG129
FMET155
FGLY157
FCYS158
FGLY159
FLYS160
FSER161
FVAL162
FILE294
FPRO321
FLEU322
FSER325

site_idAC7
Number of Residues15
DetailsBINDING SITE FOR RESIDUE ATP G 1301
ChainResidue
GSER161
GVAL162
GILE294
GPRO321
GLEU322
GSER325
GVAL125
GPHE126
GVAL127
GARG129
GMET155
GGLY157
GCYS158
GGLY159
GLYS160

site_idAC8
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM H 500
ChainResidue
HLYS13
HCYS14
HGLN16
HCYS17
HHIS18
HTHR28
HPRO30
HTHR40
HGLY41
HTYR48
HTHR49
HASN52
HTRP59
HTYR67
HLEU68
HTHR78
HLYS79
HMET80
HILE81
HPHE82

site_idAC9
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM I 500
ChainResidue
ILYS13
ICYS14
IGLN16
ICYS17
IHIS18
ITHR28
IPRO30
ITHR40
IGLY41
ITYR48
ITHR49
IASN52
ITRP59
ITYR67
ILEU68
ITHR78
ILYS79
IMET80
IILE81
IPHE82

site_idBC1
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM J 500
ChainResidue
JLYS13
JCYS14
JGLN16
JCYS17
JHIS18
JTHR28
JPRO30
JTHR40
JGLY41
JTYR48
JTHR49
JASN52
JTRP59
JTYR67
JLEU68
JTHR78
JLYS79
JMET80
JILE81
JPHE82

site_idBC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM K 500
ChainResidue
KLYS13
KCYS14
KGLN16
KCYS17
KHIS18
KTHR28
KPRO30
KTHR40
KGLY41
KTYR48
KTHR49
KASN52
KTRP59
KTYR67
KLEU68
KTHR78
KLYS79
KMET80
KILE81
KPHE82

site_idBC3
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM L 500
ChainResidue
LLYS13
LCYS14
LGLN16
LCYS17
LHIS18
LTHR28
LPRO30
LTHR40
LGLY41
LTYR48
LTHR49
LASN52
LTRP59
LTYR67
LLEU68
LTHR78
LLYS79
LMET80
LILE81
LPHE82

site_idBC4
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM M 500
ChainResidue
MLYS13
MCYS14
MGLN16
MCYS17
MHIS18
MTHR28
MPRO30
MTHR40
MGLY41
MTYR48
MTHR49
MASN52
MTRP59
MTYR67
MLEU68
MTHR78
MLYS79
MMET80
MILE81
MPHE82

site_idBC5
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEM N 500
ChainResidue
NLYS13
NCYS14
NGLN16
NCYS17
NHIS18
NTHR28
NPRO30
NTHR40
NGLY41
NTYR48
NTHR49
NASN52
NTRP59
NTYR67
NLEU68
NTHR78
NLYS79
NMET80
NILE81
NPHE82

Functional Information from PROSITE/UniProt
site_idPS00678
Number of Residues15
DetailsWD_REPEATS_1 Trp-Asp (WD) repeats signature. IATCsvDkKVKIWNS
ChainResidueDetails
AILE672-SER686
ALEU716-LEU730
ALEU758-ALA772
ALEU1142-VAL1156

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues273
DetailsRepeat: {"description":"WD 1-1"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues273
DetailsRepeat: {"description":"WD 1-2"}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues287
DetailsRepeat: {"description":"WD 1-3"}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues273
DetailsRepeat: {"description":"WD 1-4"}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues280
DetailsRepeat: {"description":"WD 1-5"}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues273
DetailsRepeat: {"description":"WD 1-6"}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues210
DetailsRepeat: {"description":"WD 1-7"}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues252
DetailsRepeat: {"description":"WD 2-1"}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues273
DetailsRepeat: {"description":"WD 2-2"}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues273
DetailsRepeat: {"description":"WD 2-3"}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues266
DetailsRepeat: {"description":"WD 2-4"}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues273
DetailsRepeat: {"description":"WD 2-5"}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues273
DetailsRepeat: {"description":"WD 2-6"}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues259
DetailsRepeat: {"description":"WD 2-7"}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues245
DetailsRepeat: {"description":"WD 2-8"}
ChainResidueDetails

site_idSWS_FT_FI16
Number of Residues77
DetailsRegion: {"description":"Interpropeller linker","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI17
Number of Residues49
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI18
Number of Residues7
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI19
Number of Residues14
DetailsBinding site: {"description":"covalent"}
ChainResidueDetails

site_idSWS_FT_FI20
Number of Residues14
DetailsBinding site: {"description":"axial binding residue"}
ChainResidueDetails

site_idSWS_FT_FI21
Number of Residues7
DetailsModified residue: {"description":"N-acetylglycine","evidences":[{"source":"PubMed","id":"5933874","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI22
Number of Residues7
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"16866357","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI23
Number of Residues7
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62897","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI24
Number of Residues7
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62897","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI25
Number of Residues7
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"18471988","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI26
Number of Residues7
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P62897","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

246704

PDB entries from 2025-12-24

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