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- PDB-8jyz: Cryo-EM structure of RCD-1 pore from Neurospora crassa -

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Basic information

Entry
Database: PDB / ID: 8jyz
TitleCryo-EM structure of RCD-1 pore from Neurospora crassa
Components
  • Gasdermin-like protein rcd-1-1
  • Gasdermin-like protein rcd-1-2
KeywordsIMMUNE SYSTEM / Pyroptosis / Gasdermnin / Pore / Allorecognition
Function / homologywide pore channel activity / programmed cell death / protein heterodimerization activity / plasma membrane / cytoplasm / Gasdermin-like protein rcd-1-2 / Gasdermin-like protein rcd-1-1
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsHou, Y.J. / Sun, Q. / Li, Y. / 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

Downloads & links

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Assembly

Deposited unit
A: Gasdermin-like protein rcd-1-1
B: Gasdermin-like protein rcd-1-2
C: Gasdermin-like protein rcd-1-1
D: Gasdermin-like protein rcd-1-2
E: Gasdermin-like protein rcd-1-1
F: Gasdermin-like protein rcd-1-2
G: Gasdermin-like protein rcd-1-1
H: Gasdermin-like protein rcd-1-2
I: Gasdermin-like protein rcd-1-1
J: Gasdermin-like protein rcd-1-2
K: Gasdermin-like protein rcd-1-1
L: Gasdermin-like protein rcd-1-2
M: Gasdermin-like protein rcd-1-1
N: Gasdermin-like protein rcd-1-2
O: Gasdermin-like protein rcd-1-1
P: Gasdermin-like protein rcd-1-2
Q: Gasdermin-like protein rcd-1-1
R: Gasdermin-like protein rcd-1-2
S: Gasdermin-like protein rcd-1-1
T: Gasdermin-like protein rcd-1-2
V: Gasdermin-like protein rcd-1-1
W: Gasdermin-like protein rcd-1-2


Theoretical massNumber of molelcules
Total (without water)625,34022
Polymers625,34022
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-like protein rcd-1-1 / Regulator of cell death 1-1


Mass: 29218.693 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: rcd-1-1, NCU05712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7SBA0
#2: Protein
Gasdermin-like protein rcd-1-2 / Regulator of cell death 1-2


Mass: 27630.418 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: rcd-1-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DW10

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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: RCD-1 pore from Neurospora crassa / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.62 MDa / Experimental value: NO
Source (natural)Organism: Neurospora crassa (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.FormulaBuffer-ID
120 mMTris1
2300 mMNaClSodium chloride1
30.5 mMTCEP1
40.2 %C12E81
SpecimenEmbedding 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: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 56 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: C11 (11 fold cyclic)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118156 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18JYX

8jyx

18JYX1PDBexperimental model
28JYY

8jyy

18JYY2PDBexperimental model
RefinementCross valid method: NONE

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