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- EMDB-7450: Cryo-EM structure of the Gasdermin A3 membrane pore -

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Basic information

Entry
Database: EMDB / ID: EMD-7450
TitleCryo-EM structure of the Gasdermin A3 membrane pore
Map dataGasdermin A3 pore with 28-fold symmetry
Sample
  • Complex: Gasdermin A3 N-terminal domain
    • Protein or peptide: Gasdermin A3
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsRuan J / Xia S / Wu H
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) releaseFeb 28, 2018-
Map releaseMay 9, 2018-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7450.png

Downloads & links

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Map

FileDownload / File: emd_7450.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGasdermin A3 pore with 28-fold symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 380 pix.
= 380. Å		1 Å/pix.
x 380 pix.
= 380. Å		1 Å/pix.
x 380 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.006133283 - 0.034187406
Average (Standard dev.)0.00011632831 (±0.0012760819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-190-190-190
Dimensions380380380
Spacing380380380
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z380.000380.000380.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-190-190-190
NC/NR/NS380380380
D min/max/mean-0.0060.0340.000

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Supplemental data

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Half map: Half map 1 of the Gasdermin A3 pore with 28-fold symmetry

Fileemd_7450_half_map_1.map
AnnotationHalf map 1 of the Gasdermin A3 pore with 28-fold symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the Gasdermin A3 pore with 28-fold symmetry

Fileemd_7450_half_map_2.map
AnnotationHalf map 2 of the Gasdermin A3 pore with 28-fold symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gasdermin A3 N-terminal domain

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

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Supramolecule #1: Gasdermin A3 N-terminal domain

SupramoleculeName: Gasdermin A3 N-terminal domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: mouse Gasdermin A3 pores with 28-fold symmetry
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 810 KDa

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Macromolecule #1: Gasdermin A3

MacromoleculeName: Gasdermin A3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHMPVFEDVT RALVRELNPR GDLTPLDSLI DFKHFRPFCL VLRKRKSTLF WGARYVRTDY TLLDLLEPGS SPSDLTDSGN FSFKNMLDVQ VQGLVEVPKT VKVKGTAGLS QSSTLEVQTL SVAPSALENL KKERKLSADH SFLNEMRYHE KNLYVVMEAV EAKQEVTVEQ ...String:
MHMPVFEDVT RALVRELNPR GDLTPLDSLI DFKHFRPFCL VLRKRKSTLF WGARYVRTDY TLLDLLEPGS SPSDLTDSGN FSFKNMLDVQ VQGLVEVPKT VKVKGTAGLS QSSTLEVQTL SVAPSALENL KKERKLSADH SFLNEMRYHE KNLYVVMEAV EAKQEVTVEQ TGNANAIFSL PSLALLGLQG SLNNNKAVTI PKGCVLAYRV RLLRVFLFNL WDIPYICNDS MQTFPKIRRV PCSAFISPTQ MISEEPEEEK LIGELEVLFQ

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

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Image processing

Final reconstructionApplied symmetry - Point group: C28 (28 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 16581
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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