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- EMDB-9948: Structure of unknow protein 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-9948
TitleStructure of unknow protein 4
Map data
Sample
  • Complex: caspase recruitment domain containing=protein 8
    • Protein or peptide: Caspase recruitment domain-containing protein 8
Keywordsfilament / SIGNALING PROTEIN
Function / homology
Function and homology information


CARD8 inflammasome complex assembly / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / negative regulation of lipopolysaccharide-mediated signaling pathway / self proteolysis ...CARD8 inflammasome complex assembly / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / negative regulation of lipopolysaccharide-mediated signaling pathway / self proteolysis / Regulation of the apoptosome activity / Hydrolases; Acting on peptide bonds (peptidases) / regulation of canonical NF-kappaB signal transduction / negative regulation of interleukin-1 beta production / pattern recognition receptor activity / negative regulation of NF-kappaB transcription factor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / antiviral innate immune response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / peptidase activity / defense response to virus / regulation of apoptotic process / protein homodimerization activity / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
FIIND domain / Function to find / FIIND domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Caspase recruitment domain-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGong Q / Xu C
Funding support Singapore, 2 items
OrganizationGrant numberCountry
Ministry of Education (Singapore)tier2 Singapore
Ministry of Education (Singapore)tier1 Singapore
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8.
Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / ...Authors: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / John Soon Yew Lim / Wah Ing Goh / Graham Wright / Franklin L Zhong / Bruno Reversade / Bin Wu /
Abstract: Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 ...Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIIND-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIIND-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIIND. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells-a process that is greatly enhanced by NLRP1-FIIND which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.
History
DepositionJun 15, 2019-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k9f
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k9f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9948.png

Downloads & links

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Map

FileDownload / File: emd_9948.map.gz / Format: CCP4 / Size: 3.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 109 pix.
= 119.9 Å		1.1 Å/pix.
x 109 pix.
= 119.9 Å		1.1 Å/pix.
x 110 pix.
= 121. Å

Surface

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0133 / Movie #1: 0.0133
Minimum - Maximum-0.0023268554 - 0.025677346
Average (Standard dev.)0.0029601478 (±0.0043605897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin656760
Dimensions109110109
Spacing110109109
CellA: 121.0 Å / B: 119.9 Å / C: 119.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z110109109
origin x/y/z0.0000.0000.000
length x/y/z121.000119.900119.900
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS676560
NC/NR/NS110109109
D min/max/mean-0.0020.0260.003

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Supplemental data

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Additional map: new additional map with ccp4 format, for model map fitting

Fileemd_9948_additional_1.map
Annotationnew additional map with ccp4 format, for model map fitting
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_9948_additional_2.map
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Half map: #2

Fileemd_9948_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_9948_half_map_2.map
Projections & Slices
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Sample components

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Entire : caspase recruitment domain containing=protein 8

EntireName: caspase recruitment domain containing=protein 8
Components
  • Complex: caspase recruitment domain containing=protein 8
    • Protein or peptide: Caspase recruitment domain-containing protein 8

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Supramolecule #1: caspase recruitment domain containing=protein 8

SupramoleculeName: caspase recruitment domain containing=protein 8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Caspase recruitment domain-containing protein 8

MacromoleculeName: Caspase recruitment domain-containing protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.445787 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGMAAFVKE NHRQLQARMG DLKGVLDDLQ DNEVLTENEK ELVEQEKTRQ SKNEALLSMV EKKGDLALDV LFRSISERDP YLVSYLRQQ NL

UniProtKB: Caspase recruitment domain-containing protein 8

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal magnification: 115000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1424 / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 1201108
Startup modelType of model: OTHER / Details: solid column
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.409 Å
Applied symmetry - Helical parameters - Δ&Phi: -99.16 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 98280
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6k9f:
Structure of unknow protein 4

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