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- PDB-2h48: Crystal structure of human caspase-1 (Cys362->Ala, Cys364->Ala, C... -

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Basic information

Entry
Database: PDB / ID: 2h48
TitleCrystal structure of human caspase-1 (Cys362->Ala, Cys364->Ala, Cys397->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)
Components
  • (Caspase 1, isoform gamma) x 2
  • N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / allosteric side / z-VAD-FMK / HYDROLASE / HYDROLASE-HYDROLASE 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
N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsScheer, J.M. / Wells, J.A. / Romanowski, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: A common allosteric site and mechanism in caspases
Authors: Scheer, J.M. / Romanowski, M.J. / Wells, J.A.
History
DepositionMay 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 1.3May 23, 2012Group: Database references
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 20, 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_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_comp_id / _struct_conn.ptnr2_auth_seq_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 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase 1, isoform gamma
B: Caspase 1, isoform gamma
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)30,5043
Polymers30,5043
Non-polymers00
Water2,918162
1
A: Caspase 1, isoform gamma
B: Caspase 1, isoform gamma
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide

A: Caspase 1, isoform gamma
B: Caspase 1, isoform gamma
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)61,0096
Polymers61,0096
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18180 Å2
ΔGint-91 kcal/mol
Surface area20870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.006, 63.006, 161.279
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-162-

HOH

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 Caspase 1, isoform gamma


Mass: 19869.838 Da / Num. of mol.: 1 / Fragment: large subunit, residues, 120-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P29466, caspase-1
#2: Protein Caspase 1, isoform gamma


Mass: 10162.559 Da / Num. of mol.: 1 / Fragment: small subunit, residues 317-404 / Mutation: C362A, C364A, C397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P29466, caspase-1
#3: Protein/peptide N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Type: Peptide-like / Class: Inhibitor / Mass: 471.907 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Pipes pH 6.0, 200 mM ammonium sulfate, 25% PEG 2000 MME, 10 mM DTT, 2 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 22, 2003
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 16802 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SC3

1sc3


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.489 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27242 829 5 %RANDOM
Rwork0.21392 ---
all0.21674 16372 --
obs0.21674 15593 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.929 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 0 162 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222140
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.9682883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.995259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92723.78995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55515385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6281515
X-RAY DIFFRACTIONr_chiral_restr0.0610.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021591
X-RAY DIFFRACTIONr_nbd_refined0.1680.2986
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.217
X-RAY DIFFRACTIONr_mcbond_it1.6082.51348
X-RAY DIFFRACTIONr_mcangle_it2.74452112
X-RAY DIFFRACTIONr_scbond_it1.4982.5886
X-RAY DIFFRACTIONr_scangle_it2.4625771
LS refinement shellResolution: 2.2→2.276 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.411 78 -
Rwork0.315 1460 -
obs--93.95 %

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