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- EMDB-7449: Cryo-EM structure of the Gasdermin A3 membrane pore -

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Basic information

Entry
Database: EMDB / ID: EMD-7449
TitleCryo-EM structure of the Gasdermin A3 membrane pore
Map dataGasdermin A3 membrane pore
Sample
  • Complex: Gasdermin A3 N domain
    • Protein or peptide: Gasdermin-A3
  • Ligand: CARDIOLIPIN
KeywordsPyroptosis / Pore forming protein / IMMUNE SYSTEM
Function / homology
Function and homology information


sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / positive regulation of extrinsic apoptotic signaling pathway / phosphatidylinositol-4-phosphate binding / skin development / hair follicle morphogenesis ...sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / positive regulation of extrinsic apoptotic signaling pathway / phosphatidylinositol-4-phosphate binding / skin development / hair follicle morphogenesis / phosphatidylserine binding / pyroptosis / somatic stem cell population maintenance / hair follicle development / extrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / mitochondrial membrane / negative regulation of canonical Wnt signaling pathway / defense response to bacterium / positive regulation of apoptotic process / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Gasdermin, pore forming domain / Gasdermin pore forming domain / Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRuan J / Wu H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)DP1HD087988 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01Al124491 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI123265 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the gasdermin A3 membrane pore.
Authors: Jianbin Ruan / Shiyu Xia / Xing Liu / Judy Lieberman / Hao Wu /
Abstract: Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of ...Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of pore formation remains unresolved. Here we present the cryo-electron microscopy structures of the 27-fold and 28-fold single-ring pores formed by the N-terminal fragment of mouse GSDMA3 (GSDMA3-NT) at 3.8 and 4.2 Å resolutions, and of a double-ring pore at 4.6 Å resolution. In the 27-fold pore, a 108-stranded anti-parallel β-barrel is formed by two β-hairpins from each subunit capped by a globular domain. We identify a positively charged helix that interacts with the acidic lipid cardiolipin. GSDMA3-NT undergoes radical conformational changes upon membrane insertion to form long, membrane-spanning β-strands. We also observe an unexpected additional symmetric ring of GSDMA3-NT subunits that does not insert into the membrane in the double-ring pore, which may represent a pre-pore state of GSDMA3-NT. These structures provide a basis that explains the activities of several mutant gasdermins, including defective mutants that are associated with cancer.
History
DepositionFeb 2, 2018-
Header (metadata) releaseMar 28, 2018-
Map releaseApr 25, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cb8
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6cb8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7449.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGasdermin A3 membrane pore
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy EMDB: 0.0119 / Movie #1: 0.03
Minimum - Maximum-0.06966423 - 0.15675774
Average (Standard dev.)0.0002948437 (±0.0036129334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-189-189-189
Dimensions380380380
Spacing380380380
CellA=B=C: 501.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z501.600501.600501.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-189-189-189
NC/NR/NS380380380
D min/max/mean-0.0700.1570.000

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Supplemental data

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Additional map: Gasdermin A3 membrane pore

Fileemd_7449_additional_1.map
AnnotationGasdermin A3 membrane pore
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Gasdermin A3 membrane pore

Fileemd_7449_additional_2.map
AnnotationGasdermin A3 membrane pore
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Gasdermin A3 N domain

EntireName: Gasdermin A3 N domain
Components
  • Complex: Gasdermin A3 N domain
    • Protein or peptide: Gasdermin-A3
  • Ligand: CARDIOLIPIN

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Supramolecule #1: Gasdermin A3 N domain

SupramoleculeName: Gasdermin A3 N domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 810 KDa

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Macromolecule #1: Gasdermin-A3

MacromoleculeName: Gasdermin-A3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 30.401035 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HMPVFEDVTR ALVRELNPRG DLTPLDSLID FKHFRPFCLV LRKRKSTLFW GARYVRTDYT LLDLLEPGSS PSDLTDSGNF SFKNMLDVQ VQGLVEVPKT VKVKGTAGLS QSSTLEVQTL SVAPSALENL KKERKLSADH SFLNEMRYHE KNLYVVMEAV E AKQEVTVE ...String:
HMPVFEDVTR ALVRELNPRG DLTPLDSLID FKHFRPFCLV LRKRKSTLFW GARYVRTDYT LLDLLEPGSS PSDLTDSGNF SFKNMLDVQ VQGLVEVPKT VKVKGTAGLS QSSTLEVQTL SVAPSALENL KKERKLSADH SFLNEMRYHE KNLYVVMEAV E AKQEVTVE QTGNANAIFS LPSLALLGLQ GSLNNNKAVT IPKGCVLAYR VRLLRVFLFN LWDIPYICND SMQTFPKIRR VP CSAFISP TQMISEEPEE EKLIGELEVL FQ

UniProtKB: Gasdermin-A3

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Macromolecule #2: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 2 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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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

Concentration2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C27 (27 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 40086
FSC plot (resolution estimation)

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