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- PDB-9c2y: Crystal Structure of JF1cpCasp2 in complex with MUR-65 -

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Basic information

Entry
Database: PDB / ID: 9c2y
TitleCrystal Structure of JF1cpCasp2 in complex with MUR-65
Components
  • JF1cpCasp2
  • MUR-65
KeywordsHYDROLASE / dimer / inhibitor / complex / peptidomimetic
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / NADE modulates death signalling / neural retina development / 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 / DNA damage response, signal transduction by p53 class mediator ...caspase-2 / endopeptidase complex / NADE modulates death signalling / neural retina development / 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 / DNA damage response, signal transduction by p53 class mediator / 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsFuller, J.L. / Finzel, B.C. / Shi, K.
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
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JF1cpCasp2
B: JF1cpCasp2
C: JF1cpCasp2
D: JF1cpCasp2
F: MUR-65
G: MUR-65
H: MUR-65
I: MUR-65


Theoretical massNumber of molelcules
Total (without water)129,5328
Polymers129,5328
Non-polymers00
Water55831
1
A: JF1cpCasp2
B: JF1cpCasp2
F: MUR-65
G: MUR-65


Theoretical massNumber of molelcules
Total (without water)64,7664
Polymers64,7664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-15 kcal/mol
Surface area18730 Å2
MethodPISA
2
C: JF1cpCasp2
D: JF1cpCasp2
H: MUR-65
I: MUR-65


Theoretical massNumber of molelcules
Total (without water)64,7664
Polymers64,7664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-16 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.288, 130.246, 78.300
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
JF1cpCasp2 / CASP-2 / Neural precursor cell expressed developmentally down-regulated protein 2 / NEDD-2 / Protease ICH-1


Mass: 31705.213 Da / Num. of mol.: 4
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
MUR-65


Mass: 677.744 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
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-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→34.051 Å / Num. obs: 41032 / % possible obs: 45.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.093 / Rrim(I) all: 0.169 / Net I/σ(I): 5.3
Reflection shellResolution: 1.963→2.29 Å / % possible obs: 6.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.712 / Num. measured all: 6044 / Num. unique obs: 1999 / Rpim(I) all: 0.475 / Rrim(I) all: 0.859 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→34.04 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 1943 4.74 %
Rwork0.1958 --
obs0.1982 41032 46.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7419 0 196 31 7646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017836
X-RAY DIFFRACTIONf_angle_d1.23910616
X-RAY DIFFRACTIONf_dihedral_angle_d9.3791098
X-RAY DIFFRACTIONf_chiral_restr0.0591170
X-RAY DIFFRACTIONf_plane_restr0.011383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.966520.303539X-RAY DIFFRACTION1
2.01-2.060.344590.3376144X-RAY DIFFRACTION2
2.06-2.120.2468250.2976261X-RAY DIFFRACTION5
2.12-2.190.3923240.3046535X-RAY DIFFRACTION9
2.19-2.270.3259430.2866846X-RAY DIFFRACTION14
2.27-2.360.307560.3061230X-RAY DIFFRACTION21
2.36-2.470.33621030.2861657X-RAY DIFFRACTION28
2.47-2.60.35461280.32474X-RAY DIFFRACTION41
2.6-2.760.29541840.28373358X-RAY DIFFRACTION56
2.76-2.970.27942450.26644867X-RAY DIFFRACTION82
2.97-3.270.30822740.23215900X-RAY DIFFRACTION98
3.27-3.750.24522790.18455905X-RAY DIFFRACTION98
3.75-4.720.20553000.14335833X-RAY DIFFRACTION98
4.72-34.040.19782710.15956040X-RAY DIFFRACTION99

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