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- EMDB-3241: Cryo-EM reconstruction of caspase-1 CARD -

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Basic information

Entry
Database: EMDB / ID: EMD-3241
TitleCryo-EM reconstruction of caspase-1 CARD
Map dataReconstruction of caspase-1 CARD filament
Sample
  • Sample: Human caspase-1 CARD
  • Protein or peptide: Caspase-1 CARD
KeywordsCaspase-1 / CARD / inflammasome / filament / cryo-EM / signalosome / helical reconstruction / death domain
Function / homology
Function and homology information


aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / DNA damage response
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily
Similarity search - Domain/homology
Uncharacterized protein YphB
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLi Y / Lu A / Schmidt FI / Yin Q / Chen S / Fu T-M / Tong AB / Ploegh HL / 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, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseMar 30, 2016-
UpdateJun 15, 2016-
Current statusJun 15, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fna
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5fna
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3241_tit...

Downloads & links

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Map

FileDownload / File: emd_3241.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of caspase-1 CARD filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 160 pix.
= 139.2 Å		0.87 Å/pix.
x 160 pix.
= 139.2 Å		0.87 Å/pix.
x 160 pix.
= 139.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.15 / Movie #1: 3.15
Minimum - Maximum-2.27765226 - 5.90264797
Average (Standard dev.)0.71799731 (±0.87744838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-79
Dimensions160160160
Spacing160160160
CellA=B=C: 139.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z139.200139.200139.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-80-80-79
NC/NR/NS160160160
D min/max/mean-2.2785.9030.718

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Supplemental data

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Sample components

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Entire : Human caspase-1 CARD

EntireName: Human caspase-1 CARD
Components
  • Sample: Human caspase-1 CARD
  • Protein or peptide: Caspase-1 CARD

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Supramolecule #1000: Human caspase-1 CARD

SupramoleculeName: Human caspase-1 CARD / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1

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Macromolecule #1: Caspase-1 CARD

MacromoleculeName: Caspase-1 CARD / type: protein_or_peptide / ID: 1 / Oligomeric state: Helical / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 DE3 / Recombinant plasmid: pDB-HIs-MBP
SequenceUniProtKB: Uncharacterized protein YphB

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8 / Details: 20 mM Sodium HEPES, pH 8.0, 150 mM NaCl, 2 mM DTT
GridDetails: holey carbon C-flat grids (R1.2/1.3, Photochip, CA), glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: blotted for 3 seconds before plunging

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Electron microscopy

MicroscopeOTHER
DateFeb 2, 2015
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Number real images: 200 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 28736 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.006 µm / Nominal defocus min: 0.001 µm
Sample stageSpecimen holder model: OTHER

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Image processing

DetailsThe particles were aligned using IHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 100.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: OTHER / Software - Name: SPIDER, IHRSR
CTF correctionDetails: Each micrograph

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