+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7451 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Gasdermin A3 membrane pore | |||||||||
Map data | Gasdermin A3 membrane pore with C27 symmetry and double-layer architecture | |||||||||
Sample |
| |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Ruan J / Xia S / Wu H | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7451.map.gz | 187.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7451-v30.xml emd-7451.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7451_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_7451.png | 63.4 KB | ||
Others | emd_7451_half_map_1.map.gz emd_7451_half_map_2.map.gz | 191.8 MB 191.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7451 | HTTPS FTP |
-Validation report
Summary document | emd_7451_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_7451_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_7451_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7451 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7451 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_7451.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Gasdermin A3 membrane pore with C27 symmetry and double-layer architecture | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1686 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: Half map 1 of the Gasdermin A3 membrane...
File | emd_7451_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 of the Gasdermin A3 membrane pore with C27 symmetry and double-layer architecture | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2 of the Gasdermin A3 membrane...
File | emd_7451_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 of the Gasdermin A3 membrane pore with C27 symmetry and double-layer architecture | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Gasdermin A3 N domain
Entire | Name: Gasdermin A3 N domain |
---|---|
Components |
|
-Supramolecule #1: Gasdermin A3 N domain
Supramolecule | Name: Gasdermin A3 N domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: mouse Gasdermin A3 pores with C27 symmetry and double-layer architecture |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 1.62 MDa |
-Macromolecule #1: Gasdermin A3
Macromolecule | Name: Gasdermin A3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 41.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |