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- PDB-4jj7: Caspase-3 specific unnatural amino acid-based peptides -

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Basic information

Entry
Database: PDB / ID: 4jj7
TitleCaspase-3 specific unnatural amino acid-based peptides
Components
  • Caspase inhibitor
  • Caspase-8
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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 / TRAIL-activated apoptotic signaling pathway / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase ...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 / TRAIL-activated apoptotic signaling pathway / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / 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 / self proteolysis / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / CLEC7A/inflammasome pathway / natural killer cell activation / negative regulation of necroptotic process / 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 / RIPK1-mediated regulated necrosis / B cell activation / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / 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 / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / 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 / lamellipodium / response to estradiol / peptidase activity / heart development / cell body / 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 / cytoplasm / cytosol
Similarity search - Function
Caspase-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / 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-8 / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACE-1MH-ASP-B3L-HLX-1U8 / DITHIANE DIOL / Caspase-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.178 Å
AuthorsVickers, C.J. / Gonzalez-Paez, G.E. / Wolan, D.W.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Selective Detection of Caspase-3 versus Caspase-7 Using Activity-Based Probes with Key Unnatural Amino Acids.
Authors: Vickers, C.J. / Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-8
B: Caspase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5754
Polymers32,2712
Non-polymers3042
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.844, 62.844, 129.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Caspase-8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH / Caspase-8 subunit p18 / Caspase-8 subunit p10


Mass: 31447.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, CASP8 MCH5, MCH5 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14790, caspase-8
#2: Protein/peptide Caspase inhibitor


Type: Peptide-like / Class: CASPASE inhibitor / Mass: 822.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: ACE-1MH-ASP-B3L-HLX-1U8
#3: Chemical ChemComp-DTD / DITHIANE DIOL


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


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE 2,6, DIMETHYLBENZOIC ACID FRAGMENT IN RESIDUE 1U8 OF THE CASPASE INHIBITOR IS REMOVED DURING ...THE 2,6, DIMETHYLBENZOIC ACID FRAGMENT IN RESIDUE 1U8 OF THE CASPASE INHIBITOR IS REMOVED DURING COVALENT ATTACHMENT TO CASPASE

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M Sodium citrate, 0.1M HEPES pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2013 / Details: mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.178→23.37 Å / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 14.04 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.178→23.365 Å / SU ML: 0.08 / σ(F): 1.36 / Phase error: 11.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1567 4671 4.97 %
Rwork0.1352 --
obs0.1363 94058 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.178→23.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 16 269 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172030
X-RAY DIFFRACTIONf_angle_d1.7342734
X-RAY DIFFRACTIONf_dihedral_angle_d14.127767
X-RAY DIFFRACTIONf_chiral_restr0.112303
X-RAY DIFFRACTIONf_plane_restr0.011352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1781-1.19150.1611180.14322816X-RAY DIFFRACTION91
1.1915-1.20550.16071540.12752988X-RAY DIFFRACTION96
1.2055-1.22020.16561490.11933042X-RAY DIFFRACTION99
1.2202-1.23560.14331350.11273135X-RAY DIFFRACTION100
1.2356-1.25190.13961380.11473112X-RAY DIFFRACTION100
1.2519-1.26910.1341550.10793075X-RAY DIFFRACTION100
1.2691-1.28720.12821700.10843059X-RAY DIFFRACTION100
1.2872-1.30640.12711570.10633103X-RAY DIFFRACTION100
1.3064-1.32680.14621650.10843051X-RAY DIFFRACTION100
1.3268-1.34860.13281820.10173060X-RAY DIFFRACTION100
1.3486-1.37180.12441760.10333088X-RAY DIFFRACTION100
1.3718-1.39670.10861700.09763133X-RAY DIFFRACTION100
1.3967-1.42360.13191460.09663077X-RAY DIFFRACTION100
1.4236-1.45270.13831730.10413058X-RAY DIFFRACTION100
1.4527-1.48420.13591620.10173119X-RAY DIFFRACTION100
1.4842-1.51880.1241400.09793085X-RAY DIFFRACTION100
1.5188-1.55670.11691710.09363099X-RAY DIFFRACTION100
1.5567-1.59880.12731760.09973092X-RAY DIFFRACTION100
1.5988-1.64590.141580.10253106X-RAY DIFFRACTION100
1.6459-1.6990.12271670.11073132X-RAY DIFFRACTION100
1.699-1.75970.13871860.11963062X-RAY DIFFRACTION100
1.7597-1.83010.15281470.1263120X-RAY DIFFRACTION100
1.8301-1.91330.14991620.13272642X-RAY DIFFRACTION85
1.9133-2.01420.16161730.13363106X-RAY DIFFRACTION99
2.0142-2.14030.14871660.13743126X-RAY DIFFRACTION100
2.1403-2.30540.1507760.14021483X-RAY DIFFRACTION47
2.3054-2.53720.17591610.15223171X-RAY DIFFRACTION100
2.5372-2.90370.18351780.17013152X-RAY DIFFRACTION100
2.9037-3.65610.16991360.16862505X-RAY DIFFRACTION97
3.6561-23.36960.20461240.16182590X-RAY DIFFRACTION86

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