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- PDB-8vp4: Crystal Structure of JF1cpCasp2 with Peptide Inhibitor AcVDVAD-CHO -

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Basic information

Entry
Database: PDB / ID: 8vp4
TitleCrystal Structure of JF1cpCasp2 with Peptide Inhibitor AcVDVAD-CHO
Components
  • AcVDVAD-CHO
  • JF1cpCasp2
KeywordsHYDROLASE / Caspase-2 / inhibitor / Alzheimer's disease / dimer
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death / : / extrinsic apoptotic signaling pathway in absence of ligand ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death / : / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / NOD1/2 Signaling Pathway / protein processing / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / nucleolus / enzyme binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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 / Death-like domain superfamily
Similarity search - Domain/homology
N-acetyl-L-valyl-L-alpha-aspartyl-L-valyl-N-[(2R)-1-carboxy-3-oxopropan-2-yl]-L-alaninamide / Caspase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsFuller, J.L. / Shi, K. / Walters, M.A. / Finzel, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R01AG062199 - 0 United States
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Reengineering of Circularly Permuted Caspase-2 to Enhance Enzyme Stability and Enable Crystallographic Studies.
Authors: Fuller, J.L. / Shi, K. / Pockes, S. / Finzel, B.C. / Ashe, K.H. / Walters, M.A.
History
DepositionJan 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JF1cpCasp2
B: JF1cpCasp2
D: AcVDVAD-CHO
C: AcVDVAD-CHO


Theoretical massNumber of molelcules
Total (without water)64,4664
Polymers64,4664
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-28 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.867, 101.548, 112.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein JF1cpCasp2


Mass: 31705.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, ICH1, NEDD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42575, caspase-2
#2: Protein/peptide AcVDVAD-CHO / AcVDVAD-CHO


Type: Peptide-like / Class: Inhibitor / Mass: 527.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-acetyl-L-valyl-L-alpha-aspartyl-L-valyl-N-[(2R)-1-carboxy-3-oxopropan-2-yl]-L-alaninamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.3 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.2 M Sodium chloride, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→37.7 Å / Num. obs: 69875 / % possible obs: 94.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.056 / Rrim(I) all: 0.158 / Net I/σ(I): 8.1
Reflection shellResolution: 1.51→1.63 Å / Rmerge(I) obs: 1.166 / Num. unique obs: 3494 / CC1/2: 0.697 / Rpim(I) all: 0.455 / Rsym value: 1.166

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158phasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→37.7 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 3463 4.96 %
Rwork0.188 --
obs0.1893 69871 68.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 0 285 4015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073847
X-RAY DIFFRACTIONf_angle_d0.9215208
X-RAY DIFFRACTIONf_dihedral_angle_d6.834541
X-RAY DIFFRACTIONf_chiral_restr0.057584
X-RAY DIFFRACTIONf_plane_restr0.008683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.408740.274771X-RAY DIFFRACTION2
1.53-1.550.2466190.2854344X-RAY DIFFRACTION9
1.55-1.570.233380.2785598X-RAY DIFFRACTION16
1.57-1.60.2607530.2417726X-RAY DIFFRACTION19
1.6-1.620.2532490.2332996X-RAY DIFFRACTION26
1.62-1.650.2438680.23291338X-RAY DIFFRACTION35
1.65-1.680.27671050.23581616X-RAY DIFFRACTION43
1.68-1.710.2674990.23051820X-RAY DIFFRACTION48
1.71-1.750.25311090.22872032X-RAY DIFFRACTION53
1.75-1.790.23881280.22952313X-RAY DIFFRACTION60
1.79-1.830.23881240.23052631X-RAY DIFFRACTION69
1.83-1.870.23961720.22242858X-RAY DIFFRACTION74
1.87-1.920.23491400.2163081X-RAY DIFFRACTION80
1.92-1.980.23811650.20323305X-RAY DIFFRACTION86
1.98-2.040.20971970.18973524X-RAY DIFFRACTION92
2.04-2.120.21352050.19073774X-RAY DIFFRACTION98
2.12-2.20.22521940.18643860X-RAY DIFFRACTION99
2.2-2.30.21711770.18493888X-RAY DIFFRACTION99
2.3-2.420.18712010.18743869X-RAY DIFFRACTION100
2.42-2.570.22692100.19333859X-RAY DIFFRACTION100
2.57-2.770.22691890.20063902X-RAY DIFFRACTION100
2.77-3.050.22042250.19723911X-RAY DIFFRACTION100
3.05-3.490.22091870.18283953X-RAY DIFFRACTION100
3.49-4.40.18681920.1553979X-RAY DIFFRACTION100
4.4-37.70.19332130.17454160X-RAY DIFFRACTION100

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