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- PDB-1pyo: Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-A... -

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Basic information

Entry
Database: PDB / ID: 1pyo
TitleCrystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho
Components
  • (Caspase-2) x 2
  • ACETYL-LEU-ASP-GLU-SER-ASJ
KeywordsHYDROLASE/HYDROLASE INHIBITOR / APOPTOSIS / CASPASE / ALPHA-BETA / THIOL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / apoptotic signaling pathway / NOD1/2 Signaling Pathway / protein processing / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / nucleolus / negative regulation of apoptotic process / enzyme binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inclusion body clearance protein Iml2/Tetratricopeptide repeat protein 39 / Iml2/Tetratricopeptide repeat protein 39 / Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site ...Inclusion body clearance protein Iml2/Tetratricopeptide repeat protein 39 / Iml2/Tetratricopeptide repeat protein 39 / Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment 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 / Death-like domain superfamily / Tetratricopeptide-like helical domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehyde / IML2-like protein YKR018C / Caspase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSchweizer, A. / Briand, C. / Grutter, M.G.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of caspase-2, apical initiator of the intrinsic apoptotic pathway.
Authors: Schweizer, A. / Briand, C. / Grutter, M.G.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jul 3, 2013Group: Structure summary
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999sequence Chains E and F represent a synthetic sequence that is commonly used for substrates and ...sequence Chains E and F represent a synthetic sequence that is commonly used for substrates and inhibitors for caspase-2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-2
B: Caspase-2
E: ACETYL-LEU-ASP-GLU-SER-ASJ
C: Caspase-2
D: Caspase-2
F: ACETYL-LEU-ASP-GLU-SER-ASJ


Theoretical massNumber of molelcules
Total (without water)62,6026
Polymers62,6026
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18000 Å2
ΔGint-88 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.649, 96.583, 97.547
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 Caspase-2 / / CASP-2 / ICH-1 protease / ICH- 1L/1S


Mass: 18790.258 Da / Num. of mol.: 2 / Fragment: subunit p18, sequence database residues 151-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2 OR ICH1 / Plasmid details: from Novagen / Plasmid: pET11d / Production host: Escherichia coli (E. coli)
Strain (production host): BL21-CodonPlus(DE3)-RIL (Stratagene)
References: UniProt: P42575, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Caspase-2 / / CASP-2 / ICH-1 protease / ICH- 1L/1S


Mass: 11920.963 Da / Num. of mol.: 2 / Fragment: subunit p12, sequence database residues 331-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2 OR ICH1 / Plasmid details: from Novagen / Plasmid: pET11d / Production host: Escherichia coli (E. coli)
Strain (production host): BL21-CodonPlus(DE3)-RIL (Stratagene)
References: UniProt: P42575, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein/peptide ACETYL-LEU-ASP-GLU-SER-ASJ


Type: Peptide-like / Class: Inhibitor / Mass: 589.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic, from Calbiochem
Source: (synth.) Saccharomyces cerevisiae (Baker's yeast) (yeast)
References: UniProt: P36114, N-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehyde
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS155 OF CHAIN A/C AND ATOM C OF ASA406 OF CHAIN E/F, ...THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS155 OF CHAIN A/C AND ATOM C OF ASA406 OF CHAIN E/F, FORMING THIOHEMIACETAL

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 6000, MOPS, DTT, SUCROSE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 %(w/v)sucrose1drop
48 mMdithiothreitol1drop
51.2-2.0 mg/mlprotein1drop
625 %(w/v)PEG60001reservoir
7100 mMMOPS1reservoirpH7.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2003 / Details: dynamically bendable mirror
RadiationMonochromator: SI(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. all: 74129 / Num. obs: 74129 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.934 Å2 / Rsym value: 0.092 / Net I/σ(I): 21.14
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 2.03 / Num. unique all: 7191 / Rsym value: 0.476 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.476

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CP3

1cp3


Resolution: 1.65→25 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1474 2 %RANDOM
Rwork0.189 ---
all-72998 --
obs-72998 100 %-
Displacement parametersBiso mean: 23.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-2.5 Å22.28 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 0 385 4566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0116
X-RAY DIFFRACTIONc_angle_deg1.5951
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 1.65→1.67 Å
RfactorNum. reflection% reflection
Rfree0.2662 40 -
Rwork0.2814 --
obs-2476 100 %
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.595
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Lowest resolution: 1.71 Å

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