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- PDB-1rwk: Crystal structure of human caspase-1 in complex with 3-(2-mercapt... -

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Basic information

Entry
Database: PDB / ID: 1rwk
TitleCrystal structure of human caspase-1 in complex with 3-(2-mercapto-acetylamino)-4-oxo-pentanoic acid
Components(Interleukin-1 beta convertase) x 2
KeywordsHYDROLASE / protein-small molecule inhibitor complex
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / microtubule / defense response to virus / endopeptidase activity / 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 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
3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRomanowski, M.J. / Lam, J.W. / Fahr, B.T. / O'Brien, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structural analysis of caspase-1 inhibitors derived from Tethering.
Authors: O'Brien, T. / Fahr, B.T. / Sopko, M.M. / Lam, J.W. / Waal, N.D. / Raimundo, B.C. / Purkey, H.E. / Pham, P. / Romanowski, M.J.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 beta convertase
B: Interleukin-1 beta convertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3343
Polymers30,1292
Non-polymers2051
Water2,900161
1
A: Interleukin-1 beta convertase
B: Interleukin-1 beta convertase
hetero molecules

A: Interleukin-1 beta convertase
B: Interleukin-1 beta convertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6686
Polymers60,2574
Non-polymers4102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17470 Å2
ΔGint-78 kcal/mol
Surface area21230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.840, 62.840, 160.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsHeterotetramer (dimer of two heterodimers). Each heterodimer is represented by chains A (the p20 subunit) and B (the p10 subunit) of human caspase-1.

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Components

#1: Protein Interleukin-1 beta convertase / IL-1BC / IL-1 beta converting enzyme / ICE / Interleukin-1 beta converting enzyme / P45 / Caspase-1 / CASP-1


Mass: 19869.838 Da / Num. of mol.: 1 / Fragment: INTERLEUKIN-1 BETA CONVERTASE P20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P29466, caspase-1
#2: Protein Interleukin-1 beta convertase / IL-1BC / IL-1 beta converting enzyme / ICE / Interleukin-1 beta converting enzyme / P45 / Caspase-1 / CASP-1


Mass: 10258.755 Da / Num. of mol.: 1 / Fragment: INTERLEUKIN-1 BETA CONVERTASE P10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P29466, caspase-1
#3: Chemical ChemComp-158 / 3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID


Mass: 205.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 274 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 2M (NH4)2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 274K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 42420 / Num. obs: 14913 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.313 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ICE

1ice


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 6.776 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.316 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25824 754 5.1 %RANDOM
Rwork0.204 ---
obs0.20669 14126 98.96 %-
all-14913 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.728 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 13 161 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212124
X-RAY DIFFRACTIONr_angle_refined_deg0.8951.9512859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825259
X-RAY DIFFRACTIONr_chiral_restr0.060.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021587
X-RAY DIFFRACTIONr_nbd_refined0.1650.2975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.2147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.216
X-RAY DIFFRACTIONr_mcbond_it1.5242.51302
X-RAY DIFFRACTIONr_mcangle_it2.6952114
X-RAY DIFFRACTIONr_scbond_it1.6212.5822
X-RAY DIFFRACTIONr_scangle_it2.6235745
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.284 91
Rwork0.223 1334

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