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- PDB-6bz9: Crystal structure of human caspase-1 in complex with Ac-FLTD-CMK -

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Basic information

Entry
Database: PDB / ID: 6bz9
TitleCrystal structure of human caspase-1 in complex with Ac-FLTD-CMK
Components
  • (Caspase-1) x 2
  • Ac-FLTD-CMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / complex / 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 / protein autoprocessing / The NLRP3 inflammasome / 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 / defense response to virus / microtubule / 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
DI(HYDROXYETHYL)ETHER / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsXiao, T.S. / Yang, J. / Liu, Z. / Wang, C. / Yang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR069908 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanism of gasdermin D recognition by inflammatory caspases and their inhibition by a gasdermin D-derived peptide inhibitor.
Authors: Yang, J. / Liu, Z. / Wang, C. / Yang, R. / Rathkey, J.K. / Pinkard, O.W. / Shi, W. / Chen, Y. / Dubyak, G.R. / Abbott, D.W. / Xiao, T.S.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 19, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
C: Ac-FLTD-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8945
Polymers30,6823
Non-polymers2122
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-36 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 63.830, 160.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 19869.838 Da / Num. of mol.: 1 / Fragment: UNP residues 120-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, caspase-1
#2: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 10258.755 Da / Num. of mol.: 1 / Fragment: UNP residues 317-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, caspase-1
#3: Protein/peptide Ac-FLTD-CMK


Mass: 553.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 53.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.796→29.66 Å / Num. obs: 31896 / % possible obs: 99.8 % / Redundancy: 21.8 % / CC1/2: 1 / Rpim(I) all: 0.013 / Net I/σ(I): 31.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 21.5 % / Mean I/σ(I) obs: 2 / CC1/2: 0.877 / Rpim(I) all: 0.375 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QBH

2qbh
PDB Unreleased entry


Resolution: 1.796→29.657 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1998 6.29 %
Rwork0.178 --
obs0.18 31762 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.796→29.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 14 125 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062166
X-RAY DIFFRACTIONf_angle_d0.7412910
X-RAY DIFFRACTIONf_dihedral_angle_d5.0791834
X-RAY DIFFRACTIONf_chiral_restr0.054320
X-RAY DIFFRACTIONf_plane_restr0.005375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7964-1.84130.34051380.28582046X-RAY DIFFRACTION97
1.8413-1.89110.24131380.23492058X-RAY DIFFRACTION99
1.8911-1.94680.20121410.212077X-RAY DIFFRACTION99
1.9468-2.00960.21511400.18632101X-RAY DIFFRACTION100
2.0096-2.08140.2381400.19492084X-RAY DIFFRACTION100
2.0814-2.16470.25981400.192084X-RAY DIFFRACTION100
2.1647-2.26320.24121420.19082119X-RAY DIFFRACTION100
2.2632-2.38250.26031410.19382099X-RAY DIFFRACTION100
2.3825-2.53160.19521420.19542126X-RAY DIFFRACTION100
2.5316-2.7270.21681430.19752127X-RAY DIFFRACTION100
2.727-3.00120.23571430.20022133X-RAY DIFFRACTION100
3.0012-3.43490.23951450.19362163X-RAY DIFFRACTION100
3.4349-4.32550.17351490.14762209X-RAY DIFFRACTION100
4.3255-29.66120.18741560.15792338X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01741.13413.47257.057-3.07093.5575-0.51121.0723-1.33160.51540.00630.18831.1160.00580.43620.7739-0.1260.15430.4023-0.16890.4922-21.3746-49.61-9.1762
22.95222.00311.84852.5987-0.40823.78860.1632-0.8037-1.3349-0.23970.16472.51810.7457-2.1422-0.20750.6504-0.3235-0.00821.018-0.09451.1427-37.1961-40.6052-9.9491
35.1462-4.9646-4.9126.97172.0847.55360.05660.9369-0.4422-0.2142-0.44970.50430.9426-0.56530.45760.3895-0.0954-0.00140.5835-0.12670.3409-25.4498-37.729-19.7432
42.61562.87260.45235.0922.00633.17220.03030.3079-0.44960.28540.3622-1.1870.14841.4996-0.31580.29150.0401-0.03510.7338-0.1010.49510.9974-31.4017-4.8669
52.69111.4611.07014.68961.54914.4794-0.0950.0868-0.18680.1960.1831-0.36420.50980.61-0.09110.31490.05690.03420.3758-0.06810.2711-7.7057-38.073-10.6386
67.14371.96241.76731.72151.14297.9014-0.0450.61530.1387-0.18330.0837-0.0968-0.20980.4689-0.0450.26740.00890.04450.3145-0.02920.3027-11.2127-28.0866-17.3107
72.6808-2.4376-3.37566.77683.39934.20410.2416-0.27220.66210.26210.3785-0.1162-0.681.0291-0.60640.4149-0.124-0.00810.5938-0.09250.4996-3.7865-21.6478-0.2315
84.53610.5488-0.14852.0733-0.07082.94470.11130.06060.5235-0.0215-0.004-0.2748-0.42460.5221-0.03350.2806-0.06780.05980.3347-0.03050.3227-10.5987-21.5938-10.3459
97.2652-1.9915-5.48472.10872.57349.1849-0.1618-0.6844-0.28690.3252-0.1951-0.03490.34531.0170.32420.3588-0.0589-0.06730.3872-0.04070.3181-10.906-25.35217.1023
105.4266-3.34563.37357.8386-5.96164.59240.09660.2595-0.038-0.33150.12260.13690.3152-0.1665-0.23930.2776-0.04420.04620.33350.00510.2491-26.0794-18.1357-16.8407
117.0445-5.12620.87887.1455-0.24252.87380.1223-0.2827-0.15930.29780.0763-0.35950.52860.6897-0.22480.36630.0363-0.04130.39950.00260.3081-7.9592-31.46325.6252
123.3574-0.3486-0.28481.73331.52746.6863-0.26710.0632-0.36360.49490.05660.25190.8107-0.10710.18760.4487-0.0330.090.220.00660.2617-21.147-37.68681.5977
137.2691.1447-1.88666.28055.01376.87260.156-0.43-0.64950.79640.1754-0.18161.15650.5763-0.22390.44590.0183-0.03440.2726-0.0120.304-15.0106-31.096110.4918
143.7348-2.5812-0.85982.83762.88814.6373-0.18820.3547-0.2463-0.0231-0.09830.76830.4913-0.51940.24360.2613-0.09980.04460.3459-0.02120.2123-27.2305-32.9106-9.7443
156.42824.8431-1.93614.10780.41748.3476-0.0086-0.49420.18030.89180.2392-1.40610.05241.1193-0.21960.54440.1922-0.1010.6794-0.14240.5227-1.5865-33.13368.1168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 151 )
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 235 )
7X-RAY DIFFRACTION7chain 'A' and (resid 236 through 245 )
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 283 )
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 297 )
10X-RAY DIFFRACTION10chain 'B' and (resid 317 through 328 )
11X-RAY DIFFRACTION11chain 'B' and (resid 329 through 347 )
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 377 )
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 390 )
14X-RAY DIFFRACTION14chain 'B' and (resid 391 through 404 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 5 )

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