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- PDB-8jyw: Cryo-EM structure of the gasdermin pore from Trichoplax adhaerens -

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Basic information

Entry
Database: PDB / ID: 8jyw
TitleCryo-EM structure of the gasdermin pore from Trichoplax adhaerens
ComponentsGasdermin pore forming domain-containing protein
KeywordsIMMUNE SYSTEM / Pyroptosis / Ggasdermin / Pore-forming
Function / homologyGasdermin-E / Gasdermin, pore forming domain / Gasdermin pore forming domain / programmed cell death / cytoplasm / Gasdermin pore forming domain-containing protein
Function and homology information
Biological speciesTrichoplax adhaerens (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHou, Y.J. / Sun, Q. / Zeng, H. / Ding, J.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gasdermin pore forming domain-containing protein
B: Gasdermin pore forming domain-containing protein
C: Gasdermin pore forming domain-containing protein
D: Gasdermin pore forming domain-containing protein
E: Gasdermin pore forming domain-containing protein
F: Gasdermin pore forming domain-containing protein
G: Gasdermin pore forming domain-containing protein
H: Gasdermin pore forming domain-containing protein
I: Gasdermin pore forming domain-containing protein
J: Gasdermin pore forming domain-containing protein
K: Gasdermin pore forming domain-containing protein
L: Gasdermin pore forming domain-containing protein
M: Gasdermin pore forming domain-containing protein
N: Gasdermin pore forming domain-containing protein
O: Gasdermin pore forming domain-containing protein
P: Gasdermin pore forming domain-containing protein
Q: Gasdermin pore forming domain-containing protein
R: Gasdermin pore forming domain-containing protein
S: Gasdermin pore forming domain-containing protein
T: Gasdermin pore forming domain-containing protein
V: Gasdermin pore forming domain-containing protein
W: Gasdermin pore forming domain-containing protein
X: Gasdermin pore forming domain-containing protein
Y: Gasdermin pore forming domain-containing protein
Z: Gasdermin pore forming domain-containing protein
AA: Gasdermin pore forming domain-containing protein
BA: Gasdermin pore forming domain-containing protein
CA: Gasdermin pore forming domain-containing protein
DA: Gasdermin pore forming domain-containing protein
EA: Gasdermin pore forming domain-containing protein
FA: Gasdermin pore forming domain-containing protein
GA: Gasdermin pore forming domain-containing protein
HA: Gasdermin pore forming domain-containing protein
IA: Gasdermin pore forming domain-containing protein
JA: Gasdermin pore forming domain-containing protein
KA: Gasdermin pore forming domain-containing protein
LA: Gasdermin pore forming domain-containing protein
MA: Gasdermin pore forming domain-containing protein
NA: Gasdermin pore forming domain-containing protein
OA: Gasdermin pore forming domain-containing protein
PA: Gasdermin pore forming domain-containing protein
QA: Gasdermin pore forming domain-containing protein
RA: Gasdermin pore forming domain-containing protein
SA: Gasdermin pore forming domain-containing protein
TA: Gasdermin pore forming domain-containing protein
UA: Gasdermin pore forming domain-containing protein
VA: Gasdermin pore forming domain-containing protein
WA: Gasdermin pore forming domain-containing protein
XA: Gasdermin pore forming domain-containing protein
YA: Gasdermin pore forming domain-containing protein
ZA: Gasdermin pore forming domain-containing protein
AB: Gasdermin pore forming domain-containing protein
BB: Gasdermin pore forming domain-containing protein
CB: Gasdermin pore forming domain-containing protein
DB: Gasdermin pore forming domain-containing protein
EB: Gasdermin pore forming domain-containing protein
FB: Gasdermin pore forming domain-containing protein
GB: Gasdermin pore forming domain-containing protein
HB: Gasdermin pore forming domain-containing protein
IB: Gasdermin pore forming domain-containing protein
JB: Gasdermin pore forming domain-containing protein
KB: Gasdermin pore forming domain-containing protein
LB: Gasdermin pore forming domain-containing protein
MB: Gasdermin pore forming domain-containing protein
NB: Gasdermin pore forming domain-containing protein
OB: Gasdermin pore forming domain-containing protein
PB: Gasdermin pore forming domain-containing protein
QB: Gasdermin pore forming domain-containing protein
RB: Gasdermin pore forming domain-containing protein
SB: Gasdermin pore forming domain-containing protein
TB: Gasdermin pore forming domain-containing protein
UB: Gasdermin pore forming domain-containing protein
VB: Gasdermin pore forming domain-containing protein
WB: Gasdermin pore forming domain-containing protein
XB: Gasdermin pore forming domain-containing protein
YB: Gasdermin pore forming domain-containing protein
ZB: Gasdermin pore forming domain-containing protein
AC: Gasdermin pore forming domain-containing protein
BC: Gasdermin pore forming domain-containing protein
CC: Gasdermin pore forming domain-containing protein
DC: Gasdermin pore forming domain-containing protein
EC: Gasdermin pore forming domain-containing protein
FC: Gasdermin pore forming domain-containing protein
GC: Gasdermin pore forming domain-containing protein
HC: Gasdermin pore forming domain-containing protein
IC: Gasdermin pore forming domain-containing protein
JC: Gasdermin pore forming domain-containing protein
KC: Gasdermin pore forming domain-containing protein


Theoretical massNumber of molelcules
Total (without water)2,394,77588
Polymers2,394,77588
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Gasdermin pore forming domain-containing protein


Mass: 27213.355 Da / Num. of mol.: 88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: TRIADDRAFT_52857 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3RMM6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gasdermin pore from Trichoplax adhaerens / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Trichoplax adhaerens (invertebrata)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
Buffer component
IDConc.FormulaBuffer-ID
120 mMHEPES1
2150 mMNaClSodium chloride1
30.5 % (w/v)DDM1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D44 (2x44 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52901 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8JYV

8jyv


Accession code: 8JYV / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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