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- PDB-4quh: Caspase-3 T140G -

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Basic information

Entry
Database: PDB / ID: 4quh
TitleCaspase-3 T140G
Components
  • ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
  • Caspase-3Caspase 3
  • short peptde
Keywordshydrolase/hydrolase inhibitor / Allosteric Network / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / 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 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / 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 / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / pyroptotic inflammatory response / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / response to amino acid / cell fate commitment / Pyroptosis / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / response to nicotine / apoptotic signaling pathway / hippocampus development / sensory perception of sound / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / protein processing / neuron differentiation / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / response to hypoxia / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Asp-CMK / AZIDE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
C: Caspase-3
D: short peptde
I: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
J: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,36412
Polymers64,8055
Non-polymers5597
Water7,584421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.973, 96.845, 68.866
Angle α, β, γ (deg.)90.00, 129.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-505-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Caspase-3 / 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: 31607.883 Da / Num. of mol.: 2 / Mutation: T140G
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

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Protein/peptide , 2 types, 3 molecules DIJ

#2: Protein/peptide short peptde


Mass: 519.461 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: 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

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Non-polymers , 4 types, 428 molecules

#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.72 %
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 291 by the hanging drop vapor diffusion method using 4 L 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

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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: 1.759→36.456 Å / Num. all: 56387 / Num. obs: 56387 / % possible obs: 99.16 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.76-1.79193.3
1.79-1.82197.5
1.82-1.86198.9
1.86-1.9199.6
1.9-1.941100
1.94-1.981100

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Processing

Software
NameVersionClassification
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.759→36.456 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 1997 3.54 %Random
Rwork0.1536 ---
obs0.1548 56387 99.16 %-
all-56387 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.759→36.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 36 421 4328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074101
X-RAY DIFFRACTIONf_angle_d1.0675530
X-RAY DIFFRACTIONf_dihedral_angle_d13.3951560
X-RAY DIFFRACTIONf_chiral_restr0.049596
X-RAY DIFFRACTIONf_plane_restr0.004709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7587-1.80270.2251330.19153604X-RAY DIFFRACTION93
1.8027-1.85140.21471460.18243831X-RAY DIFFRACTION98
1.8514-1.90590.23161370.17113900X-RAY DIFFRACTION99
1.9059-1.96740.18661480.16093915X-RAY DIFFRACTION100
1.9674-2.03770.20561430.15753853X-RAY DIFFRACTION100
2.0377-2.11930.19241460.15643890X-RAY DIFFRACTION100
2.1193-2.21580.18431400.15483939X-RAY DIFFRACTION100
2.2158-2.33260.19011450.15373907X-RAY DIFFRACTION100
2.3326-2.47870.19421470.15563892X-RAY DIFFRACTION100
2.4787-2.670.16961420.16463925X-RAY DIFFRACTION100
2.67-2.93860.22671370.16743902X-RAY DIFFRACTION100
2.9386-3.36360.1711430.15713925X-RAY DIFFRACTION100
3.3636-4.23670.1591470.12513925X-RAY DIFFRACTION100
4.2367-36.46380.17431430.14463982X-RAY DIFFRACTION99

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