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- EMDB-36734: Cryo-EM structure of RCD-1 pore from Neurospora crassa -

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Basic information

Entry
Database: EMDB / ID: EMD-36734
TitleCryo-EM structure of RCD-1 pore from Neurospora crassa
Map data
Sample
  • Complex: RCD-1 pore from Neurospora crassa
    • Protein or peptide: Gasdermin-like protein rcd-1-1
    • Protein or peptide: Gasdermin-like protein rcd-1-2
KeywordsPyroptosis / Gasdermnin / Pore / Allorecognition / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsHou YJ / Sun Q / Li Y / 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_36734.png

Downloads & links

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Map

FileDownload / File: emd_36734.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å		1.07 Å/pix.
x 380 pix.
= 406.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.7799306 - 4.042685
Average (Standard dev.)0.001525738 (±0.08611175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 406.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36734_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_36734_half_map_2.map
Projections & Slices
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Sample components

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Entire : RCD-1 pore from Neurospora crassa

EntireName: RCD-1 pore from Neurospora crassa
Components
  • Complex: RCD-1 pore from Neurospora crassa
    • Protein or peptide: Gasdermin-like protein rcd-1-1
    • Protein or peptide: Gasdermin-like protein rcd-1-2

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Supramolecule #1: RCD-1 pore from Neurospora crassa

SupramoleculeName: RCD-1 pore from Neurospora crassa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 620 KDa

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Macromolecule #1: Gasdermin-like protein rcd-1-1

MacromoleculeName: Gasdermin-like protein rcd-1-1 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 29.218693 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SGRPMDKCWF TLDNAHYPPP SLDSMRSGHP ISPASLGHLI PSLAHLDQII NAKAIEPFPA TMDIHGPTII EDFKWDHSHE YSLSLGGKV PIPLAPAGVP FVDLNVGLGG AFSRSVANYW EFDRLERYIM QPTRSYVQKC IERDEVKRWI AKNKSMMMMG R WEVYMITG ...String:
SGRPMDKCWF TLDNAHYPPP SLDSMRSGHP ISPASLGHLI PSLAHLDQII NAKAIEPFPA TMDIHGPTII EDFKWDHSHE YSLSLGGKV PIPLAPAGVP FVDLNVGLGG AFSRSVANYW EFDRLERYIM QPTRSYVQKC IERDEVKRWI AKNKSMMMMG R WEVYMITG IIVARGGGRK KKEKTTGKEF SVEVTVEVPL IVEAGPGGKR NTARQKTWGT SQTGDFVWAV RLAKITKSGL HS DWKMETV FGKTSSFRGQ KAIF

UniProtKB: Gasdermin-like protein rcd-1-1

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Macromolecule #2: Gasdermin-like protein rcd-1-2

MacromoleculeName: Gasdermin-like protein rcd-1-2 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Neurospora crassa (fungus)
Molecular weightTheoretical: 27.630418 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SGRPMDNEEW FPLKQTHYPP PTIPSMKTGH PTGPISIGHI IPDLRHLDNV INCKGFEPFP PNMDVFTAHY EQCHFGDHLN SEFVVQAKA AAPIENIVPG VDVTGSAGLH HTNITSDRWE YDSVVEYAVY PTRQYIDRLL ESKEVRQYIQ KSKKLLGGWC V YMVTGIMV ...String:
SGRPMDNEEW FPLKQTHYPP PTIPSMKTGH PTGPISIGHI IPDLRHLDNV INCKGFEPFP PNMDVFTAHY EQCHFGDHLN SEFVVQAKA AAPIENIVPG VDVTGSAGLH HTNITSDRWE YDSVVEYAVY PTRQYIDRLL ESKEVRQYIQ KSKKLLGGWC V YMVTGIMV ARGGGRNVTS EEKGAGVSGN VGFQVPGIGE FAPEVGWDTK TKTKVNAHHT TDFVCAIRLV KIAKSGLRSS WT MKKVTRE F

UniProtKB: Gasdermin-like protein rcd-1-2

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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: 8
Component:
ConcentrationFormula
20.0 mMTris
300.0 mMNaCl
0.5 mMTCEP
0.2 %C12E8
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: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 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: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8jyx

source_name: PDB, initial_model_type: experimental model

8jyy

source_name: PDB, initial_model_type: experimental model
Output model

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

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