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- PDB-1qtn: CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTI... -

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Basic information

Entry
Database: PDB / ID: 1qtn
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE INHIBITOR ACE-IETD-ALDEHYDE
Components
  • (CASPASE-8Caspase 8) x 2
  • ACETYL-ILE-GLU-THR-ASP-ALDEHYDE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / APOPTOSIS / DITHIANE-DIOL / CASPASE / CYSTEINE-PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria ...caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / self proteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / natural killer cell activation / negative regulation of necroptotic process / CLEC7A/inflammasome pathway / activation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / cysteine-type endopeptidase activity involved in apoptotic process / TNFR1-induced proapoptotic signaling / execution phase of apoptosis / regulation of innate immune response / RIPK1-mediated regulated necrosis / B cell activation / pyroptosis / Apoptotic cleavage of cellular proteins / positive regulation of proteolysis / macrophage differentiation / protein maturation / cellular response to organic cyclic compound / extrinsic apoptotic signaling pathway via death domain receptors / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / cysteine-type peptidase activity / negative regulation of canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / regulation of cytokine production / T cell activation / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / response to estradiol / lamellipodium / cell body / heart development / peptidase activity / scaffold protein binding / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / cytoskeleton / 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 / nucleoplasm / identical protein binding / cytosol / cytoplasm
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-(2-oxoethyl)-L-isoleucyl-L-alpha-glutamyl-N-[(1R)-2-carboxy-1-formylethyl]-L-threoninamide / DITHIANE DIOL / Caspase-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.2 Å
AuthorsWatt, W. / Watenpaugh, K.D.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The atomic-resolution structure 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
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: 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 1.3Apr 4, 2012Group: Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CASPASE-8
B: CASPASE-8
C: ACETYL-ILE-GLU-THR-ASP-ALDEHYDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3345
Polymers30,0303
Non-polymers3042
Water5,981332
1
A: CASPASE-8
B: CASPASE-8
C: ACETYL-ILE-GLU-THR-ASP-ALDEHYDE
hetero molecules

A: CASPASE-8
B: CASPASE-8
C: ACETYL-ILE-GLU-THR-ASP-ALDEHYDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,66910
Polymers60,0606
Non-polymers6094
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)62.400, 62.400, 129.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-725-

HOH

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Components

#1: Protein CASPASE-8 / Caspase 8


Mass: 18640.119 Da / Num. of mol.: 1 / Fragment: P18 FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q14790, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein CASPASE-8 / Caspase 8


Mass: 10901.364 Da / Num. of mol.: 1 / Fragment: P11 FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q14790, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein/peptide ACETYL-ILE-GLU-THR-ASP-ALDEHYDE


Type: Peptide-like / Class: Inhibitor / Mass: 488.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
References: N-(2-oxoethyl)-L-isoleucyl-L-alpha-glutamyl-N-[(1R)-2-carboxy-1-formylethyl]-L-threoninamide
#4: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS360A AND ATOM C OF ASJ504C, FORMING A THIOHEMIACETAL

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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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 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, ...Details: 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
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.4 mg/mlprotein1drop
220 mMTris1drop
3100 mMdithiothreitol1drop
41.4 Msodium citrate1reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.03
DetectorType: BRUKER / Detector: CCD / Date: Sep 9, 1998 / Details: NON-FOCUSING
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 79890 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 3.73 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.35 / % possible all: 82
Reflection
*PLUS
Num. measured all: 298890

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
SMARTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 1CP3

1cp3


Resolution: 1.2→8 Å / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3981 5.3 %0.53% OF REFLECTIONS
Rwork0.143 ---
all0.166 75433 --
obs0.166 60671 87 %-
Solvent computationSolvent model: SWAT
Refinement stepCycle: LAST / Resolution: 1.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 16 332 2319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.2
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.2
X-RAY DIFFRACTIONs_zero_chiral_vol0.2
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / % reflection Rfree: 5.3 % / Rfactor obs: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.2
X-RAY DIFFRACTIONs_planar_d0.2
X-RAY DIFFRACTIONs_plane_restr0.2

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