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- EMDB-36733: Cryo-EM structure of the gasdermin pore from Trichoplax adhaerens -

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Basic information

Entry
Database: EMDB / ID: EMD-36733
TitleCryo-EM structure of the gasdermin pore from Trichoplax adhaerens
Map data
Sample
  • Complex: Gasdermin pore from Trichoplax adhaerens
    • Protein or peptide: Gasdermin protein from Trichoplax adhaerens
KeywordsPyroptosis / Ggasdermin / Pore-forming / IMMUNE SYSTEM
Function / homologyGasdermin-E / Gasdermin, pore forming domain / Gasdermin pore forming domain / programmed cell death / Gasdermin pore forming domain-containing protein
Function and homology information
Biological speciesTrichoplax adhaerens (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsHou YJ / Sun Q / Zeng H / Ding J
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Science / Year: 2024
Title: Cleavage-independent activation of ancient eukaryotic gasdermins and structural mechanisms.
Authors: Yueyue Li / Yanjie Hou / Qi Sun / Huan Zeng / Fanyi Meng / Xiang Tian / Qun He / Feng Shao / Jingjin Ding /
Abstract: Gasdermins (GSDMs) are pore-forming proteins that execute pyroptosis for immune defense. GSDMs are two-domain proteins activated by proteolytic removal of the inhibitory domain. In this work, we ...Gasdermins (GSDMs) are pore-forming proteins that execute pyroptosis for immune defense. GSDMs are two-domain proteins activated by proteolytic removal of the inhibitory domain. In this work, we report two types of cleavage-independent GSDM activation. First, GSDM, a pore-forming domain-only protein from the basal metazoan , is a disulfides-linked autoinhibited dimer activated by reduction of the disulfides. The cryo-electron microscopy (cryo-EM) structure illustrates the assembly mechanism for the 44-mer GSDM pore. Second, RCD-1-1 and RCD-1-2, encoded by the polymorphic () gene in filamentous fungus , are also pore-forming domain-only GSDMs. RCD-1-1 and RCD-1-2, when encountering each other, form pores and cause pyroptosis, underlying allorecognition in . The cryo-EM structure reveals a pore of 11 RCD-1-1/RCD-1-2 heterodimers and a heterodimerization-triggered pore assembly mechanism. This study shows mechanistic diversities in GSDM activation and indicates versatile functions of GSDMs.
History
DepositionJul 4, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36733.png

Downloads & links

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Map

FileDownload / File: emd_36733.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.05427081 - 0.08384303
Average (Standard dev.)0.00022883083 (±0.0037483978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36733_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_36733_half_map_2.map
Projections & Slices
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Sample components

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Entire : Gasdermin pore from Trichoplax adhaerens

EntireName: Gasdermin pore from Trichoplax adhaerens
Components
  • Complex: Gasdermin pore from Trichoplax adhaerens
    • Protein or peptide: Gasdermin protein from Trichoplax adhaerens

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Supramolecule #1: Gasdermin pore from Trichoplax adhaerens

SupramoleculeName: Gasdermin pore from Trichoplax adhaerens / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trichoplax adhaerens (invertebrata)

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Macromolecule #1: Gasdermin protein from Trichoplax adhaerens

MacromoleculeName: Gasdermin protein from Trichoplax adhaerens / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Trichoplax adhaerens (invertebrata)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SGRPMFAVAV NEFIRSAGQD SLCGVPDINS SGDFMPLHII VKEVPKVLPC CRRPKIKRTP YTLNDILDEP CPNQLKSSDL VTFTEPLVS NVKASSSIGL QILKHFDSGA KGSKNFITSA SLGTVVKAET IDITKVLAKV RTAKAKVEND LVSRVMKTKR L CLGLVVET ...String:
SGRPMFAVAV NEFIRSAGQD SLCGVPDINS SGDFMPLHII VKEVPKVLPC CRRPKIKRTP YTLNDILDEP CPNQLKSSDL VTFTEPLVS NVKASSSIGL QILKHFDSGA KGSKNFITSA SLGTVVKAET IDITKVLAKV RTAKAKVEND LVSRVMKTKR L CLGLVVET ACVAAAGKLT EADNWEISGH TNANIGEAVV TATAELDKNL SRKIEIPPGT ALAYSFMDLE ILEDRSLRVS SS AGAMFDS GKAESTV

UniProtKB: Gasdermin pore forming domain-containing protein

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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

Concentration0.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormula
20.0 mMHEPES
150.0 mMNaCl
0.5 % (w/v)DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D41 (2x41 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30428
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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