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- PDB-1f9e: CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF ... -

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Basic information

Entry
Database: PDB / ID: 1f9e
TitleCASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO
Components
  • (PHQ)DEVD
  • Caspase-8 subunit p10
  • Caspase-8 subunit p18
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / CASPASE-8 / FLICE / MCH5 / MACH / APOPTOSIS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / ripoptosome / Defective RIPK1-mediated regulated necrosis ...caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / self proteolysis / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / CLEC7A/inflammasome pathway / death-inducing signaling complex / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / natural killer cell activation / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / response to anesthetic / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / response to tumor necrosis factor / B cell activation / positive regulation of proteolysis / macrophage differentiation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / Caspase-mediated cleavage of cytoskeletal proteins / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / regulation of cytokine production / proteolysis involved in protein catabolic process / T cell activation / protein maturation / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / protein processing / Regulation of necroptotic cell death / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / lamellipodium / heart development / cell body / scaffold protein binding / response to ethanol / angiogenesis / response to lipopolysaccharide / mitochondrial outer membrane / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-L-alpha-aspartyl-L-alpha-glutamyl-L-valyl-L-aspartic acid / Caspase-8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsBlanchard, H. / Donepudi, M. / Tschopp, M. / Kodandapani, L. / Wu, J.C. / Grutter, M.G.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Caspase-8 specificity probed at subsite S(4): crystal structure of the caspase-8-Z-DEVD-cho complex.
Authors: Blanchard, H. / Donepudi, M. / Tschopp, M. / Kodandapani, L. / Wu, J.C. / Grutter, M.G.
#1: Journal: Structure / Year: 1999
Title: The three-dimensional structure of caspase-8: an initiator enzyme in apoptosis
Authors: Blanchard, H. / Kodandapani, L. / Mittl, P.R.E. / Marco, S.D. / Krebs, J.F. / Wu, J.C. / Tomaselli, K.J. / Gruetter, M.G.
#2: Journal: Structure / Year: 1999
Title: The atomic-resolution of human caspase-8, a key activator of apoptosis.
Authors: Watt, W. / Koeplinger, K.A. / Mildner, A.M. / Heinrikson, R.L. / Tomasselli, A.G. / Watenpaugh, K.D.
History
DepositionJul 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_entry_details.has_protein_modification / _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_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-8 subunit p18
B: Caspase-8 subunit p10
Q: (PHQ)DEVD
C: Caspase-8 subunit p18
D: Caspase-8 subunit p10
R: (PHQ)DEVD
E: Caspase-8 subunit p18
F: Caspase-8 subunit p10
S: (PHQ)DEVD
G: Caspase-8 subunit p18
H: Caspase-8 subunit p10
T: (PHQ)DEVD
I: Caspase-8 subunit p18
J: Caspase-8 subunit p10
U: (PHQ)DEVD
K: Caspase-8 subunit p18
L: Caspase-8 subunit p10
V: (PHQ)DEVD


Theoretical massNumber of molelcules
Total (without water)169,82218
Polymers169,82218
Non-polymers00
Water84747
1
A: Caspase-8 subunit p18
B: Caspase-8 subunit p10
Q: (PHQ)DEVD
C: Caspase-8 subunit p18
D: Caspase-8 subunit p10
R: (PHQ)DEVD


Theoretical massNumber of molelcules
Total (without water)56,6076
Polymers56,6076
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16630 Å2
ΔGint-81 kcal/mol
Surface area18540 Å2
MethodPISA
2
E: Caspase-8 subunit p18
F: Caspase-8 subunit p10
S: (PHQ)DEVD
G: Caspase-8 subunit p18
H: Caspase-8 subunit p10
T: (PHQ)DEVD


Theoretical massNumber of molelcules
Total (without water)56,6076
Polymers56,6076
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-80 kcal/mol
Surface area18370 Å2
MethodPISA
3
I: Caspase-8 subunit p18
J: Caspase-8 subunit p10
U: (PHQ)DEVD
K: Caspase-8 subunit p18
L: Caspase-8 subunit p10
V: (PHQ)DEVD


Theoretical massNumber of molelcules
Total (without water)56,6076
Polymers56,6076
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-78 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.029, 188.748, 209.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsEach caspase-8 molecule is a tetramer consisting of 2(p18/p12) chains.

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Components

#1: Protein
Caspase-8 subunit p18


Mass: 17416.957 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, MCH5 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: Q14790
#2: Protein
Caspase-8 subunit p10


Mass: 10273.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, MCH5 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: Q14790
#3: Protein/peptide
(PHQ)DEVD


Type: Peptide-like / Class: Inhibitor / Mass: 613.013 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic (others)
References: N-[(benzyloxy)carbonyl]-L-alpha-aspartyl-L-alpha-glutamyl-L-valyl-L-aspartic acid, UniProt: Q14790*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS285 OF CHAIN A/C/E/G/I/K/ AND ATOM C OF THE TERMINAL ...THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS285 OF CHAIN A/C/E/G/I/K/ AND ATOM C OF THE TERMINAL ASA OF CHAIN Q/R/S/T/U/V, FORMING THIOHEMIACETAL
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1-propanol, sodium citrate, MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
230 %(w/v)1-propanol1reservoir
3200 mMsodium citrate1reservoir
4100 mMMES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 42891 / Num. obs: 42872 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.6
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.537 / Num. unique all: 2839 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 213414
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 2839 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→19.94 Å / σ(F): 0
Stereochemistry target values: CNS_TOPPAR:protein_rep.param CNS_TOPPAR:water_rep.param CNS_TOPPAR:protein.top CNS_TOPPAR:water.top topology.pro (inhibitor topology) parameter.pro (inhibitor parameters)
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4318 -RANDOM
Rwork0.241 ---
all-43103 --
obs-42872 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11879 0 0 47 11926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_torsion_deg23.1
X-RAY DIFFRACTIONc_torsion_impr_deg1.83
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / σ(F): 0 / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6

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