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5l08

Cryo-EM structure of Casp-8 tDED filament

Method: ELECTRON MICROSCOPY Dmax: 117.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Caspase-8

Homo sapiens

UniProt Q14790

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain A； UniProt 60–243 Chain B； UniProt 60–243 Chain C； UniProt 60–243 Chain D； UniProt 60–243 Chain E； UniProt 60–243 Chain F； UniProt 60–243 Chain G； UniProt 60–243 Chain H； UniProt 60–243 Chain I； UniProt 60–243 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5L08 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1F9E CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO Deposited 2000-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 222–374（153 aa）
Chain B 390–478（89 aa）
Chain C 222–374（153 aa）
Chain D 390–478（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K
Resolution 2.90 Å R-free 0.289
1F9E CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO Deposited 2000-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 222–374（153 aa）
Chain F 390–478（89 aa）
Chain G 222–374（153 aa）
Chain H 390–478（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K
Resolution 2.90 Å R-free 0.289
1F9E CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO Deposited 2000-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 222–374（153 aa）
Chain J 390–478（89 aa）
Chain K 222–374（153 aa）
Chain L 390–478（89 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K
Resolution 2.90 Å R-free 0.289
1I4E CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX Deposited 2001-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 222–479（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.296
1I4E CRYSTAL STRUCTURE OF THE CASPASE-8/P35 COMPLEX Deposited 2001-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 222–479（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.296
1QDU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK Deposited 1999-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 222–374（153 aa）
Chain B 390–477（88 aa）
Chain C 222–374（153 aa）
Chain D 390–477（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；300mM ammonium phosphate, 27% (w/v) isopropanol, 100mM sodium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.302
1QDU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK Deposited 1999-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 222–374（153 aa）
Chain F 390–477（88 aa）
Chain G 222–374（153 aa）
Chain H 390–477（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；300mM ammonium phosphate, 27% (w/v) isopropanol, 100mM sodium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.302
1QDU CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK Deposited 1999-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 222–374（153 aa）
Chain J 390–477（88 aa）
Chain K 222–374（153 aa）
Chain L 390–477（88 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；300mM ammonium phosphate, 27% (w/v) isopropanol, 100mM sodium phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.302
1QTN CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE Deposited 1999-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 223–374（152 aa） Fragment：P18 FRAGMENT
Chain B 390–479（90 aa） Fragment：P11 FRAGMENT
Not recorded DTD DITHIANE DIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；282 K；3 MICROLITERS PROTEIN (8.4 MG/ ML IN 20 MM TRISHCL, 100MM DTT AT PH 8.0) MIXED WITH 3 MICROLITERS WELL BUFFER (1.4 SODIUM CITRATE, 0.1M HEPES, AT PH 8.0) AT 4 DEG. C, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Resolution 1.20 Å R-free 0.188
2C2Z Crystal structure of caspase-8 in complex with aza-peptide Michael acceptor inhibitor Deposited 2005-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 218–374（157 aa） Fragment：ALPHA SUB-UNIT, RESIDUES 218-374
Chain B 376–479（104 aa） Fragment：BETA-SUBUNIT, RESIDUES 376-479
Not recorded DTD DITHIANE DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；1.4M SODIUM CITRATE, 100MM HEPES PH 8.0
Resolution 1.95 Å R-free 0.187
2FUN alternative p35-caspase-8 complex Deposited 2006-01-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 222–479（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K
Resolution 3.00 Å R-free 0.260
2FUN alternative p35-caspase-8 complex Deposited 2006-01-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 222–479（258 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 295K
Resolution 3.00 Å R-free 0.260
2K7Z Solution Structure of the Catalytic Domain of Procaspase-8 Deposited 2008-08-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 217–479（263 aa） Fragment：UNP residues 213-479
Mutation：C360A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；305 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] procaspase8, 10 mM DTT, 100 mM sodium chloride, 20 mM [U-2H] TRIS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N; 80% 2H] procaspase8, 10 mM DTT, 100 mM sodium chloride, 20 mM [U-2H] TRIS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2Y1L Caspase-8 in Complex with DARPin-8.4 Deposited 2010-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: octameric
Chain A 217–374（158 aa） Fragment：P18 SUBUNIT, RESIDUES 218-374
Chain B 376–479（104 aa） Fragment：P10 SUBUNIT, RESIDUES 376-479
Chain C 217–374（158 aa） Fragment：P18 SUBUNIT, RESIDUES 218-374
Chain D 376–479（104 aa） Fragment：P10 SUBUNIT, RESIDUES 376-479
Not recorded SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；100 MM CITRIC ACID PH 4.9 (RT), 200 MM LI2SO4, 22.5% PEG 4K.
Resolution 1.80 Å R-free 0.218
3H11 Zymogen caspase-8:c-FLIPL protease domain complex Deposited 2009-04-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 217–479（263 aa）
Mutation：D359A, D369A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；293 K；0.9 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), 0.2 M lithium sulfate, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.250
3KJN Caspase 8 bound to a covalent inhibitor Deposited 2009-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 211–374（164 aa） Fragment：residues 211-374
Chain B 385–479（95 aa） Fragment：residues 385-479
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 B93 (3S)-3-({[(5S)-2-{2-[(1H-benzimidazol-5-ylcarbonyl)amino]ethyl}-7-(cyclohexylmethyl)-1,3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazin-5-yl]carbonyl}amino)-4-oxopentanoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K
Resolution 1.80 Å R-free 0.202
3KJQ Caspase 8 with covalent inhibitor Deposited 2009-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 211–374（164 aa）
Chain B 385–479（95 aa）
Not recorded B94 (3S)-3-({[(5S,8R)-2-(3-carboxypropyl)-8-(2-{[(4-chlorophenyl)acetyl]amino}ethyl)-1,3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazin-5-yl]carbonyl}amino)-4-oxopentanoic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；277 K；2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K
Resolution 1.80 Å R-free 0.207
4JJ7 Caspase-3 specific unnatural amino acid-based peptides Deposited 2013-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 217–479（263 aa）
Not recorded DTD DITHIANE DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；1 M Sodium citrate, 0.1M HEPES pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.18 Å R-free 0.157
4PRZ Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 217–479（263 aa） Fragment：UNP RESIDUES 217-479
Not recorded DTD DITHIANE DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；1.0 M sodium citrate, 0.1 M HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.12 Å R-free 0.218
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 217–479（263 aa） Fragment：UNP RESIDUES 217-479
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.73 Å R-free 0.185
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 217–479（263 aa） Fragment：UNP RESIDUES 217-479
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.73 Å R-free 0.185
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 217–479（263 aa） Fragment：UNP RESIDUES 217-479
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.73 Å R-free 0.185
4PS1 Caspase-8 specific unnatural amino acid peptides Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 217–479（263 aa） Fragment：UNP RESIDUES 217-479
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M Sodium citrate, pH 5.5, 36% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.73 Å R-free 0.185
4ZBW Crystal structure of death effector domain of Caspase8 in Homo Sapiens Deposited 2015-04-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 61–247（187 aa）
Chain B 61–247（187 aa）
Mutation：F122A, I128D Mutation：F122A, I128D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；0.2M sodium chloride, 25% PEG3350
Resolution 2.20 Å R-free 0.251
5H31 Structural basis for dimerization of the death effector domains of Caspase-8 Deposited 2016-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–188（188 aa） Fragment：UNP residues 1-188
Chain B 1–188（188 aa） Fragment：UNP residues 1-188
Mutation：F122A Mutation：F122A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；100 mM sodium chloride, 100 mM Tris, 21% PEG3350, 10 mM Sarcosine,
Resolution 3.17 Å R-free 0.268
5H31 Structural basis for dimerization of the death effector domains of Caspase-8 Deposited 2016-10-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–188（188 aa） Fragment：UNP residues 1-188
Chain D 1–188（188 aa） Fragment：UNP residues 1-188
Mutation：F122A Mutation：F122A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；100 mM sodium chloride, 100 mM Tris, 21% PEG3350, 10 mM Sarcosine,
Resolution 3.17 Å R-free 0.268
5H33 Structural basis for dimerization of the death effector domains of Caspase-8 Deposited 2016-10-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–188（188 aa）
Chain B 1–188（188 aa）
Mutation：F122A Mutation：F122A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；293 K；50mM sodium chloride, 100mM Tris pH 8.5, 22.5% PEG3350
Resolution 3.60 Å R-free 0.313
5JQE Crystal structure of caspase8 tDED Deposited 2016-05-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–186（186 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；293 K；0.1M MMT buffer, pH 8.0, 25% PEG 1500
Resolution 3.16 Å R-free 0.274
6AGW Pro-domain of Caspase-8 Deposited 2018-08-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–180（180 aa） Fragment：UNP residues 1-180
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；(NH4)2SO4, Cacodylate, NaCl
Resolution 2.09 Å R-free 0.269
6PX9 Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R Deposited 2019-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 276–538（263 aa） Fragment：UNP residues 276-538
Chain B 276–538（263 aa） Fragment：UNP residues 276-538
Mutation：D374A, D384A, C409S, C433S Mutation：D374A, D384A, C409S, C433S 63R N-{(3R)-1-[4-(morpholin-4-yl)benzene-1-carbonyl]piperidin-3-yl}-N-phenylacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M imidazole, pH 8.0, 1.0 M sodium citrate
Resolution 2.88 Å R-free 0.366
6PX9 Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R Deposited 2019-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 276–538（263 aa） Fragment：UNP residues 276-538
Chain D 276–538（263 aa） Fragment：UNP residues 276-538
Mutation：D374A, D384A, C409S, C433S Mutation：D374A, D384A, C409S, C433S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M imidazole, pH 8.0, 1.0 M sodium citrate
Resolution 2.88 Å R-free 0.366
6PX9 Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R Deposited 2019-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 276–538（263 aa） Fragment：UNP residues 276-538
Chain F 276–538（263 aa） Fragment：UNP residues 276-538
Mutation：D374A, D384A, C409S, C433S Mutation：D374A, D384A, C409S, C433S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M imidazole, pH 8.0, 1.0 M sodium citrate
Resolution 2.88 Å R-free 0.366
6X8H Caspase-8 in complex with AOMK inhibitor, Ac-DW3-KE, forms tetrahedral adduct Deposited 2020-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 276–443（168 aa） Fragment：p18 (UNP residues 276-443)
Chain B 444–538（95 aa） Fragment：p10 (UNP residues 444-538)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；295 K；1:1 protein : 0.10 M HEPES, 1.0 M sodium citrate
Resolution 1.48 Å R-free 0.167
7LVM CASP8 isoform B DED domain Deposited 2021-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–188（187 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；100mM Hepes pH 7.5, 20% Ethylene Glycol, 18% PEG 3350, 200mM Sodium Chloride
Resolution 1.47 Å R-free 0.233
8YBX Structure of the FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–479（479 aa）
Chain B 1–479（479 aa）
Chain C 1–479（479 aa）
Mutation：F122G/L123G, C360A, D374A, D384A Mutation：F122G/L123G, C360A, D374A, D384A Mutation：F122G/L123G, C360A, D374A, D384A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
8YD7 Structure of FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–185（185 aa）
Chain B 1–185（185 aa）
Chain C 1–185（185 aa）
Chain D 1–185（185 aa）
Chain E 1–185（185 aa）
Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G,L123G Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；HEPES, TBG, PEG8000, TCEP, sodium chloride
Resolution 3.32 Å R-free 0.231
8YD8 Structure of FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-02-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–185（185 aa）
Chain B 1–185（185 aa）
Chain C 1–185（185 aa）
Chain D 1–185（185 aa）
Chain E 1–185（185 aa）
Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；HEPES, PEG 8000, TBG, TCEP, sodium chloride
Resolution 3.11 Å R-free 0.241
8YM4 Structure of Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–185（185 aa）
Chain B 1–185（185 aa）
Chain C 1–185（185 aa）
Chain D 1–185（185 aa）
Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) SE SELENIUM ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 0.08 M sodium chloride, 0.2 M Potassium Thiocyanate, 10 % PEG 4000, 0.01 M TCEP
Resolution 2.34 Å R-free 0.253
8YM5 Structure of Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–185（185 aa）
Chain B 1–185（185 aa）
Chain C 1–185（185 aa）
Chain D 1–185（185 aa）
Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：F122G, L123G Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 0.08 M sodium chloride, 0.2 M Potassium Thiocyanate, 10 % PEG 4000, 0.01 M TCEP
Resolution 2.09 Å R-free 0.231
8YM6 Structure of Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 1–185（185 aa）
Chain B 1–185（185 aa）
Chain C 1–185（185 aa）
Chain D 1–185（185 aa）
Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G Mutation：F122G, L123G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M HEPES pH 7.5, 0.2 M Lithium chloride, 20 % PEG 400, 0.1 M TBG pH 9.0
Resolution 3.30 Å R-free 0.264
8YNI Structure of the FADD/Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric
Chain A 1–479（479 aa）
Chain B 1–479（479 aa）
Chain C 1–479（479 aa）
Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8YNK Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–479（479 aa）
Chain B 1–479（479 aa）
Chain C 1–479（479 aa）
Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
8YNL Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–479（479 aa）
Chain B 1–479（479 aa）
Chain C 1–479（479 aa）
Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8YNM Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–479（479 aa）
Chain B 1–479（479 aa）
Chain C 1–479（479 aa）
Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
8YNN Structure of the Caspase-8/cFLIP death effector domain assembly Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–479（479 aa）
Chain B 1–479（479 aa）
Chain C 1–479（479 aa）
Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A Mutation：F122G, L123G, C360A, D374A, D384A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å

33 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CASP8_HUMAN
Isoform Q14790-9
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–184； UniProt 60–243 Author chain B； PDBConstruct 1–184； UniProt 60–243 Author chain C； PDBConstruct 1–184； UniProt 60–243 Author chain D； PDBConstruct 1–184； UniProt 60–243 Author chain E； PDBConstruct 1–184； UniProt 60–243 Author chain F； PDBConstruct 1–184； UniProt 60–243 Author chain G； PDBConstruct 1–184； UniProt 60–243 Author chain H； PDBConstruct 1–184； UniProt 60–243 Author chain I； PDBConstruct 1–184； UniProt 60–243

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5l08

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l08
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5l08
Deposition date deposition_date2016-07-26
Structure title titleCryo-EM structure of Casp-8 tDED filament
Keywords keywordsCasp-8, filament, DED, Death domain, APOPTOSIS; APOPTOSIS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.39 Å
Radius of gyration Rg (electron density) rg_electron37.40 Å
Forward intensity I(0) i0541243000.00
Molecular weight molecular_weight194040.0 kDa
Excluded volume excluded_volume245390 ų
Envelope volume envelope_volume332600 ų
Hydration-shell volume shell_volume71224 ų
Envelope diameter envelope_diameter129.3 Å
Shell Rg shell_rg45.78 Å
Envelope Rg envelope_rg36.63 Å
Shape Rg shape_rg37.41 Å
Total Rg total_rg37.92 Å
Total atoms total_atoms13617
Residues n_residues1629
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax117.9 Å
Rg (real space) rg_real38.10 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real5.4120e+08
I(0) uncertainty (real space) i0_real_error8.8440e+06
Rg (reciprocal space) rg_reciprocal38.28 Å
I(0) (reciprocal space) i0_reciprocal541300000.0000
Solution quality estimate total_estimate0.6824
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.8 Å
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.356
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha137600000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.961; Smooth: 0.857
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)