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- PDB-5fna: Cryo-EM reconstruction of caspase-1 CARD -

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Basic information

Entry
Database: PDB / ID: 5fna
TitleCryo-EM reconstruction of caspase-1 CARD
ComponentsCaspase-1Caspase 1
KeywordsHYDROLASE / CARD / INFLAMMASOME / FILAMENT / SIGNALOSOME / HELICAL RECONSTRUCTION / DEATH DOMAIN
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 / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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. ...Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLi, Y. / Lu, A. / Schmidt, F.I. / Yin, Q. / Chen, S. / Fu, T.M. / Tong, A.B. / Ploegh, H.L. / Mao, Y. / Wu, H.
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Molecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism.
Authors: Alvin Lu / Yang Li / Florian I Schmidt / Qian Yin / Shuobing Chen / Tian-Min Fu / Alexander B Tong / Hidde L Ploegh / Youdong Mao / Hao Wu /
Abstract: Inflammasomes are cytosolic caspase-1-activation complexes that sense intrinsic and extrinsic danger signals, and trigger inflammatory responses and pyroptotic cell death. Homotypic interactions ...Inflammasomes are cytosolic caspase-1-activation complexes that sense intrinsic and extrinsic danger signals, and trigger inflammatory responses and pyroptotic cell death. Homotypic interactions among Pyrin domains and caspase recruitment domains (CARDs) in inflammasome-complex components mediate oligomerization into filamentous assemblies. Several cytosolic proteins consisting of only interaction domains exert inhibitory effects on inflammasome assembly. In this study, we determined the structure of the human caspase-1 CARD domain (caspase-1(CARD)) filament by cryo-electron microscopy and investigated the biophysical properties of two caspase-1-like CARD-only proteins: human inhibitor of CARD (INCA or CARD17) and ICEBERG (CARD18). Our results reveal that INCA caps caspase-1 filaments, thereby exerting potent inhibition with low-nanomolar Ki on caspase-1(CARD) polymerization in vitro and inflammasome activation in cells. Whereas caspase-1(CARD) uses six complementary surfaces of three types for filament assembly, INCA is defective in two of the six interfaces and thus terminates the caspase-1 filament.
History
DepositionNov 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3May 18, 2016Group: Database references
Revision 1.4Aug 30, 2017Group: Data collection / Category: em_imaging / em_software
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.image_processing_id
Revision 1.5Sep 11, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
C: Caspase-1
D: Caspase-1
E: Caspase-1
F: Caspase-1
G: Caspase-1
H: Caspase-1


Theoretical massNumber of molelcules
Total (without water)76,7218
Polymers76,7218
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
Caspase-1 / 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: 9590.171 Da / Num. of mol.: 8 / Fragment: CARD DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: PDB-HIS-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29466, caspase-1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: CASPASE-1 CARD / Type: COMPLEX
Buffer solutionName: 20 MM SODIUM HEPES, 150 MM NACL, 2 MM DTT / pH: 8 / Details: 20 MM SODIUM HEPES, 150 MM NACL, 2 MM DTT
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA / Date: Feb 2, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 28736 X / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)
Image scansNum. digital images: 200

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Processing

EM software
IDNameCategory
1IHRSR3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
3D reconstructionMethod: IHRSR / Resolution: 4.8 Å / Num. of particles: 69222 / Actual pixel size: 0.87 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3241. (DEPOSITION ID: 14034).
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--EM
RefinementHighest resolution: 4.8 Å
Refinement stepCycle: LAST / Highest resolution: 4.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 0 0 0 5328

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