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- EMDB-35591: Human NLRP1 complexed with thioredoxin (focused map) -

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Basic information

Entry
Database: EMDB / ID: EMD-35591
TitleHuman NLRP1 complexed with thioredoxin (focused map)
Map dataB-factor sharpened map
Sample
  • Complex: hNLRP1 complexed with sfTRX
    • Complex: hNLRP1
    • Complex: sfTRX
KeywordsNLRP1 / inflammasome / thioredoxin / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Spodoptera frugiperda (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsZhang Z / Ohto U
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2023
Title: Structural basis for thioredoxin-mediated suppression of NLRP1 inflammasome.
Authors: Zhikuan Zhang / Takuma Shibata / Akiko Fujimura / Jiro Kitaura / Kensuke Miyake / Umeharu Ohto / Toshiyuki Shimizu /
Abstract: Inflammasome sensors detect pathogen- and danger-associated molecular patterns and promote inflammation and pyroptosis. NLRP1 was the first inflammasome sensor to be described, and its ...Inflammasome sensors detect pathogen- and danger-associated molecular patterns and promote inflammation and pyroptosis. NLRP1 was the first inflammasome sensor to be described, and its hyperactivation is linked to autoinflammatory disease and cancer. However, the mechanism underlying the activation and regulation of NLRP1 has not been clearly elucidated. Here we identify ubiquitously expressed endogenous thioredoxin (TRX) as a binder of NLRP1 and a suppressor of the NLRP1 inflammasome. The cryo-electron microscopy structure of human NLRP1 shows NLRP1 bound to Spodoptera frugiperda TRX. Mutagenesis studies of NLRP1 and human TRX show that TRX in the oxidized form binds to the nucleotide-binding domain subdomain of NLRP1. This observation highlights the crucial role of redox-active cysteines of TRX in NLRP1 binding. Cellular assays reveal that TRX suppresses NLRP1 inflammasome activation and thus negatively regulates NLRP1. Our data identify the TRX system as an intrinsic checkpoint for innate immunity and provide opportunities for future therapeutic intervention in NLRP1 inflammasome activation targeting this system.
History
DepositionMar 8, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35591.png

Downloads & links

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Map

FileDownload / File: emd_35591.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 160 pix.
= 199.2 Å		1.25 Å/pix.
x 160 pix.
= 199.2 Å		1.25 Å/pix.
x 160 pix.
= 199.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.21508715 - 0.38627338
Average (Standard dev.)0.00021719506 (±0.007092612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35591_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_35591_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35591_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35591_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hNLRP1 complexed with sfTRX

EntireName: hNLRP1 complexed with sfTRX
Components
  • Complex: hNLRP1 complexed with sfTRX
    • Complex: hNLRP1
    • Complex: sfTRX

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Supramolecule #1: hNLRP1 complexed with sfTRX

SupramoleculeName: hNLRP1 complexed with sfTRX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: hNLRP1

SupramoleculeName: hNLRP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: sfTRX

SupramoleculeName: sfTRX / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72304
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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