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- PDB-1ice: STRUCTURE AND MECHANISM OF INTERLEUKIN-1BETA CONVERTING ENZYME -

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Basic information

Entry
Database: PDB / ID: 1ice
TitleSTRUCTURE AND MECHANISM OF INTERLEUKIN-1BETA CONVERTING ENZYME
Components
  • (INTERLEUKIN-1 BETA CONVERTING ENZYME) x 2
  • TETRAPEPTIDE ALDEHYDE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYTOKINE / 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 / NLRP1 inflammasome complex / icosanoid biosynthetic process / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / NLRP1 inflammasome complex / icosanoid biosynthetic process / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / caspase binding / osmosensory signaling pathway / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / Interleukin-37 signaling / pattern recognition receptor signaling pathway / cellular response to organic substance / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein autoprocessing / protein maturation / The NLRP3 inflammasome / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / positive regulation of inflammatory response / cellular response to type II interferon / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / cellular response to lipopolysaccharide / microtubule / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Tyr-Val-Ala-Asp-Aldehyde / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsWilson, K.P. / Griffith, J.P. / Kim, E.E. / Navia, M.A.
CitationJournal: Nature / Year: 1994
Title: Structure and mechanism of interleukin-1 beta converting enzyme.
Authors: Wilson, K.P. / Black, J.A. / Thomson, J.A. / Kim, E.E. / Griffith, J.P. / Navia, M.A. / Murcko, M.A. / Chambers, S.P. / Aldape, R.A. / Raybuck, S.A.
History
DepositionSep 29, 1994-
Revision 1.0Jul 28, 1995Provider: 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 1.3Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA CONVERTING ENZYME
T: TETRAPEPTIDE ALDEHYDE
B: INTERLEUKIN-1 BETA CONVERTING ENZYME


Theoretical massNumber of molelcules
Total (without water)29,5463
Polymers29,5463
Non-polymers00
Water61334
1
A: INTERLEUKIN-1 BETA CONVERTING ENZYME
T: TETRAPEPTIDE ALDEHYDE
B: INTERLEUKIN-1 BETA CONVERTING ENZYME

A: INTERLEUKIN-1 BETA CONVERTING ENZYME
T: TETRAPEPTIDE ALDEHYDE
B: INTERLEUKIN-1 BETA CONVERTING ENZYME


Theoretical massNumber of molelcules
Total (without water)59,0926
Polymers59,0926
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18110 Å2
ΔGint-106 kcal/mol
Surface area20160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.400, 64.400, 163.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: LYS A 296 - ASP A 297 OMEGA = 109.96 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein INTERLEUKIN-1 BETA CONVERTING ENZYME


Mass: 18810.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P29466, caspase-1
#2: Protein/peptide TETRAPEPTIDE ALDEHYDE


Type: Peptide-like / Class: Inhibitor / Mass: 476.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Ac-Tyr-Val-Ala-Asp-Aldehyde
#3: Protein INTERLEUKIN-1 BETA CONVERTING ENZYME


Mass: 10258.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P29466, caspase-1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DISULFIDE BOND BETWEEN CYS 136 AND CYS 363 REPORTED HERE IS OBSERVED IN SOME OF THE X-RAY DATA ...THE DISULFIDE BOND BETWEEN CYS 136 AND CYS 363 REPORTED HERE IS OBSERVED IN SOME OF THE X-RAY DATA SETS, BUT NOT ALL. THE TWO RESIDUES REMAIN ADJACENT TO ONE ANOTHER IN THOSE INSTANCES WHERE THE SIDE CHAINS ARE NOT POSITIONED TO FORM THE S-S BOND. THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS285A AND ATOM C OF ASA289T, FORMING A THIOHEMIACETAL

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMcitrate1drop
32.0 mMDTT1drop
415 %PEG40001reservoir
5400 mM1reservoirLi2SO4
6200 mMsodium HEPES1reservoir
75 mMsodium cacodylate1reservoir
80.5 %beta-octyl glucoside1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / % possible obs: 90 % / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→7 Å / σ(F): 1
Details: THE ICE STRUCTURE WAS SOLVED WITH A TETRAPEPTIDE ALDEHYDE REPRESENTED BY CHAIN T COVALENTLY ATTACHED TO THE SULPHUR ATOM OF CYSTEINE 285.
RfactorNum. reflection
Rwork0.19 -
obs0.19 9123
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 0 34 2096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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