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- PDB-1ibc: CRYSTAL STRUCTURE OF INHIBITED INTERLEUKIN-1BETA CONVERTING ENZYME -

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Basic information

Entry
Database: PDB / ID: 1ibc
TitleCRYSTAL STRUCTURE OF INHIBITED INTERLEUKIN-1BETA CONVERTING ENZYME
Components
  • (INTERLEUKIN-1BETA CONVERTING ENZYME) x 2
  • PEPTIDE ACE-TRP-GLU-HIS-ASA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / CYSTEINE PROTEASE / INTERLEUKIN-1BETA CONVERTING ENZYME / ICE / CASPASE-1 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex / positive regulation of interleukin-18 production / CARD domain binding / cytokine precursor processing / NLRP3 inflammasome complex / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / positive regulation of tumor necrosis factor-mediated signaling pathway / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cytokine binding / protein autoprocessing / The NLRP3 inflammasome / Pyroptosis / Purinergic signaling in leishmaniasis infection / protein maturation / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / cellular response to type II interferon / kinase binding / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / cellular response to lipopolysaccharide / regulation of inflammatory response / regulation of apoptotic process / endopeptidase activity / defense response to virus / microtubule / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.73 Å
AuthorsBecker, J.W. / Rotonda, J.
Citation
Journal: Chem.Biol. / Year: 1997
Title: A combinatorial approach for determining protease specificities: application to interleukin-1beta converting enzyme (ICE).
Authors: Rano, T.A. / Timkey, T. / Peterson, E.P. / Rotonda, J. / Nicholson, D.W. / Becker, J.W. / Chapman, K.T. / Thornberry, N.A.
#1: Journal: Protein Sci. / Year: 1995
Title: Interleukin-1 Beta Converting Enzyme: A Novel Cysteine Protease Required for Il-1 Beta Production and Implicated in Programmed Cell Death
Authors: Thornberry, N.A. / Molineaux, S.M.
History
DepositionFeb 12, 1997Processing site: BNL
Revision 1.0Feb 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-1BETA CONVERTING ENZYME
B: INTERLEUKIN-1BETA CONVERTING ENZYME
C: PEPTIDE ACE-TRP-GLU-HIS-ASA


Theoretical massNumber of molelcules
Total (without water)32,2943
Polymers32,2943
Non-polymers00
Water68538
1
A: INTERLEUKIN-1BETA CONVERTING ENZYME
B: INTERLEUKIN-1BETA CONVERTING ENZYME
C: PEPTIDE ACE-TRP-GLU-HIS-ASA

A: INTERLEUKIN-1BETA CONVERTING ENZYME
B: INTERLEUKIN-1BETA CONVERTING ENZYME
C: PEPTIDE ACE-TRP-GLU-HIS-ASA


Theoretical massNumber of molelcules
Total (without water)64,5886
Polymers64,5886
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18180 Å2
ΔGint-105 kcal/mol
Surface area20610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.610, 64.610, 160.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-702-

HOH

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Components

#1: Protein INTERLEUKIN-1BETA CONVERTING ENZYME / ICE / CASPASE-1


Mass: 21482.574 Da / Num. of mol.: 1 / Mutation: D381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P29466, caspase-1
#2: Protein INTERLEUKIN-1BETA CONVERTING ENZYME / ICE / CASPASE-1


Mass: 10214.745 Da / Num. of mol.: 1 / Mutation: D381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P29466, caspase-1
#3: Protein/peptide PEPTIDE ACE-TRP-GLU-HIS-ASA


Mass: 596.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.72 Å3/Da / Density % sol: 58 %
Crystal growpH: 8.5
Details: 1.5 ML DROPS OF PROTEIN-INHIBITOR SOLUTION (5.0 MG/ML IN 10 MILLIMOLAR TRIS-HCL, PH 8.5, 10 MILLI-MOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7. ...Details: 1.5 ML DROPS OF PROTEIN-INHIBITOR SOLUTION (5.0 MG/ML IN 10 MILLIMOLAR TRIS-HCL, PH 8.5, 10 MILLI-MOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7.2% PEG-6000 (W:W), 0.10 M PIPES PH 5.8, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.0 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMdithiothreitol1drop
43 mM1dropNaN3
57.2 %(w/w)PEG60001reservoir
60.10 MPIPES1reservoir
710 mMdithiothreitol1reservoir
83 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 9, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8445 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.96 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.047
Reflection
*PLUS
Highest resolution: 2.73 Å / % possible obs: 87 % / Num. measured all: 26257
Reflection shell
*PLUS
Highest resolution: 2.73 Å / Lowest resolution: 2.83 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SAINTdata reduction
SAINTdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: ICE INHIBITED BY ACE-YVAD-CHO

Resolution: 2.73→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 863 10.7 %RANDOM
Rwork0.173 ---
obs0.173 8078 84.4 %-
Displacement parametersBiso mean: 33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.26 Å
Luzzati d res low-20 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 0 38 2111
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it7.361.5
X-RAY DIFFRACTIONx_mcangle_it11.062
X-RAY DIFFRACTIONx_scbond_it10.612
X-RAY DIFFRACTIONx_scangle_it15.182.5
LS refinement shellResolution: 2.73→2.83 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 25 9.5 %
Rwork0.255 239 -
obs--28.5 %
Xplor fileSerial no: 1 / Param file: ICE288.PAR / Topol file: ICE288.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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