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- PDB-4qui: Caspase-3 F128AV266H -

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Basic information

Entry
Database: PDB / ID: 4qui
TitleCaspase-3 F128AV266H
Components
  • ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
  • Caspase-3
Keywordshydrolase/hydrolase inhibitor / Allosteric Network / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cellular response to staurosporine / cyclin-dependent protein serine/threonine kinase inhibitor activity / death-inducing signaling complex / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / death receptor binding / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / response to anesthetic / execution phase of apoptosis / negative regulation of cytokine production / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / pyroptotic inflammatory response / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / response to tumor necrosis factor / negative regulation of cell cycle / T cell homeostasis / B cell homeostasis / cell fate commitment / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to X-ray / response to amino acid / response to glucose / response to UV / keratinocyte differentiation / Degradation of the extracellular matrix / striated muscle cell differentiation / intrinsic apoptotic signaling pathway / response to glucocorticoid / protein maturation / erythrocyte differentiation / response to nicotine / hippocampus development / apoptotic signaling pathway / enzyme activator activity / response to hydrogen peroxide / protein catabolic process / sensory perception of sound / regulation of protein stability / protein processing / response to wounding / neuron differentiation / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / postsynaptic density / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #1460 / Peptidase C14 family / 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 ...Rossmann fold - #1460 / Peptidase C14 family / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Asp-CMK / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.758 Å
AuthorsCade, C. / Swartz, P.D. / MacKenzie, S.H. / Clark, A.C.
CitationJournal: Biochemistry / Year: 2014
Title: Modifying caspase-3 activity by altering allosteric networks.
Authors: Cade, C. / Swartz, P. / MacKenzie, S.H. / Clark, A.C.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / 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_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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-3
B: Caspase-3
D: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
C: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9058
Polymers64,5264
Non-polymers3794
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Caspase-3
D: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
hetero molecules

B: Caspase-3
C: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9058
Polymers64,5264
Non-polymers3794
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_563-x,y+1,-z-21
Buried area4830 Å2
ΔGint-39 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.285, 85.017, 68.994
Angle α, β, γ (deg.)90.00, 125.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Caspase-3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1 / Caspase-3 subunit p17 / Caspase-3 subunit p12


Mass: 31728.012 Da / Num. of mol.: 2 / Mutation: F128A, V266H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein/peptide ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Asp-CMK
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ...Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 18 oC by the hanging drop vapor diffusion method using 4 uL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2012
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.758→33.872 Å / Num. all: 53266 / Num. obs: 53266 / % possible obs: 96.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.758→33.872 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 1991 3.74 %
Rwork0.1498 --
obs0.1514 53266 96.59 %
all-53266 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.758→33.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 18 463 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064438
X-RAY DIFFRACTIONf_angle_d1.0396015
X-RAY DIFFRACTIONf_dihedral_angle_d12.6891717
X-RAY DIFFRACTIONf_chiral_restr0.045652
X-RAY DIFFRACTIONf_plane_restr0.004773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7577-1.80160.26451330.20643378X-RAY DIFFRACTION89
1.8016-1.85040.24581370.19653582X-RAY DIFFRACTION94
1.8504-1.90480.28951350.18113604X-RAY DIFFRACTION96
1.9048-1.96630.21861440.17623657X-RAY DIFFRACTION96
1.9663-2.03650.22561390.15853632X-RAY DIFFRACTION96
2.0365-2.11810.1941420.15343618X-RAY DIFFRACTION97
2.1181-2.21450.19741390.15383695X-RAY DIFFRACTION97
2.2145-2.33120.20431470.14793682X-RAY DIFFRACTION97
2.3312-2.47720.23141420.153683X-RAY DIFFRACTION98
2.4772-2.66840.19711450.15253700X-RAY DIFFRACTION98
2.6684-2.93680.19581450.15693727X-RAY DIFFRACTION98
2.9368-3.36140.18181440.15533742X-RAY DIFFRACTION98
3.3614-4.23370.15191460.12323770X-RAY DIFFRACTION99
4.2337-33.87840.16571530.13573805X-RAY DIFFRACTION98

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