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- PDB-5i9t: Caspase 3 V266C -

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Basic information

Entry
Database: PDB / ID: 5i9t
TitleCaspase 3 V266C
Components
  • ACE-ASP-GLU-VAL-ASK
  • Caspase-3
KeywordsHydrolase/Hydrolase Inhibitor / Allostery / saturation mutagenesis / conformational selection / native ensemble / protein solvation / protein structure / protein dynamics / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Stimulation of the cell death response by PAK-2p34 / caspase-3 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / positive regulation of pyroptotic inflammatory response / NADE modulates death signalling / luteolysis ...Stimulation of the cell death response by PAK-2p34 / caspase-3 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / positive regulation of pyroptotic inflammatory response / NADE modulates death signalling / luteolysis / response to cobalt ion / : / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / 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 / death receptor binding / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / : / fibroblast apoptotic process / epithelial cell apoptotic process / negative regulation of cytokine production / platelet formation / Other interleukin signaling / execution phase of apoptosis / positive regulation of amyloid-beta formation / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of activated T cell proliferation / T cell homeostasis / B cell homeostasis / neurotrophin TRK receptor signaling pathway / negative regulation of cell cycle / protein maturation / response to X-ray / response to amino acid / cell fate commitment / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / enzyme activator activity / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / apoptotic signaling pathway / hippocampus development / response to nicotine / sensory perception of sound / regulation of protein stability / protein catabolic process / response to hydrogen peroxide / protein processing / neuron differentiation / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / 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 / ACETATE ION / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsMaciag, J.J. / Mackenzie, S.H. / Tucker, M.B. / Schipper, J.L. / Swartz, P.D. / Clark, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection.
Authors: Maciag, J.J. / Mackenzie, S.H. / Tucker, M.B. / Schipper, J.L. / Swartz, P. / Clark, A.C.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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 / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: ACE-ASP-GLU-VAL-ASK
E: ACE-ASP-GLU-VAL-ASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6675
Polymers64,6084
Non-polymers591
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-16 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.315, 96.299, 68.019
Angle α, β, γ (deg.)90.00, 128.90, 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 / SCA-1


Mass: 31769.105 Da / Num. of mol.: 2 / Mutation: V266C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32
Production host: Escherichia coli str. 'clone D i14' (bacteria)
References: UniProt: P42574, caspase-3
#2: Protein/peptide ACE-ASP-GLU-VAL-ASK


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) / References: Ac-Asp-Glu-Val-Asp-CMK
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Caspase-3 variants were crystallized in the presence of Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING ...Details: Caspase-3 variants were crystallized in the presence of Ac-DEVD-CMK. PROTEINS WERE DIALYZED IN A BUFFER OF 10 MM TRIS-HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML USING AMICON ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR, AC-DEVD-CMK RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT, INHIBITOR TO PEPTIDE. 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 WAS 10 MM TRIS-HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF CONCENTRATED PROTEIN WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM SODIUM CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V. SOLUTIONS WERE INCUBATED AT 18 DEG C USING THE HANGING DROP METHOD. CRYSTALS GREW WITHIN THREE DAYS FOR WILD- TYPE CASPASE-3 AND WITHIN TWO WEEKS FOR THE MUTANTS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.949→33.581 Å / Num. obs: 39516 / % possible obs: 99.6 % / Redundancy: 3.8 % / Net I/σ(I): 1.34

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.95→33.58 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.01
Details: Authors state that there is a fundamental incompatibility in the naming of the inhibitor structure and the refinement program cannot be made to establish a bond that exists between the ...Details: Authors state that there is a fundamental incompatibility in the naming of the inhibitor structure and the refinement program cannot be made to establish a bond that exists between the inhibitor and the protein at the active site cysteine.
RfactorNum. reflection% reflection
Rfree0.198 2013 5.09 %
Rwork0.164 --
obs0.166 39516 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 4 349 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074122
X-RAY DIFFRACTIONf_angle_d0.8455565
X-RAY DIFFRACTIONf_dihedral_angle_d16.3772536
X-RAY DIFFRACTIONf_chiral_restr0.054605
X-RAY DIFFRACTIONf_plane_restr0.005714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9489-1.99760.28711370.21322599X-RAY DIFFRACTION96
1.9976-2.05160.26751450.20872668X-RAY DIFFRACTION100
2.0516-2.1120.29281420.22492650X-RAY DIFFRACTION100
2.112-2.18010.23221460.18542672X-RAY DIFFRACTION100
2.1801-2.2580.26661440.20452697X-RAY DIFFRACTION100
2.258-2.34840.20181450.17082669X-RAY DIFFRACTION100
2.3484-2.45530.19591420.15832679X-RAY DIFFRACTION100
2.4553-2.58470.19811450.15492680X-RAY DIFFRACTION100
2.5847-2.74650.20381430.16022659X-RAY DIFFRACTION100
2.7465-2.95850.18481420.16362688X-RAY DIFFRACTION100
2.9585-3.2560.19531450.15592711X-RAY DIFFRACTION100
3.256-3.72660.15981430.14552672X-RAY DIFFRACTION100
3.7266-4.69310.15161450.12692710X-RAY DIFFRACTION100
4.6931-33.58630.18241490.16932749X-RAY DIFFRACTION100

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