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- EMDB-3018: Cryo-EM single particle 3D reconstruction of the induced, monomer... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3018 | |||||||||
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Title | Cryo-EM single particle 3D reconstruction of the induced, monomeric conformation of E. coli alpha-2-macroglobulin (ECAM) | |||||||||
![]() | Reconstruction of induced monomeric Escherichia coli alpha-2-macroglobulin | |||||||||
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![]() | alpha-2-macroglobulin / ECAM / peptidase inhibitor | |||||||||
Function / homology | ![]() endopeptidase inhibitor activity / protein homodimerization activity / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
![]() | Garcia Ferrer I / Arede P / Gomez Blanco J / Luque D / Duquerroy S / Caston JR / Goulas T / Gomis Ruth FX | |||||||||
![]() | ![]() Title: Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition. Authors: Irene Garcia-Ferrer / Pedro Arêde / Josué Gómez-Blanco / Daniel Luque / Stephane Duquerroy / José R Castón / Theodoros Goulas / F Xavier Gomis-Rüth / ![]() ![]() Abstract: The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2- ...The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2-macroglobulin (α2M). Escherichia coli α2M (ECAM) is a ∼ 180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric "snap trap." | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.1 KB 9.1 KB | Display Display | ![]() |
Images | ![]() | 34.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 209.3 KB | Display | ![]() |
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Full document | ![]() | 208.5 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3016C ![]() 3017C ![]() 4ziqC ![]() 4ziuC ![]() 4zjgC ![]() 4zjhC ![]() 5a42C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of induced monomeric Escherichia coli alpha-2-macroglobulin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Induced, monomeric conformation of the E. coli alpha-2-macroglobu...
Entire | Name: Induced, monomeric conformation of the E. coli alpha-2-macroglobulin (ECAM). |
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Components |
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-Supramolecule #1000: Induced, monomeric conformation of the E. coli alpha-2-macroglobu...
Supramolecule | Name: Induced, monomeric conformation of the E. coli alpha-2-macroglobulin (ECAM). type: sample / ID: 1000 / Oligomeric state: Monomeric / Number unique components: 1 |
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Molecular weight | Experimental: 180 KDa / Theoretical: 180 KDa / Method: Size exclusion chromatography. |
-Macromolecule #1: alpha-2-macroglobulin
Macromolecule | Name: alpha-2-macroglobulin / type: protein_or_peptide / ID: 1 / Name.synonym: ECAM Details: ECAM was reacted with trypsin and the resulting induced, monomeric ECAM was purified by size-exclusion chromatography. Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 180 KDa / Theoretical: 180 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Alpha-2-macroglobulin |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.4 / Details: 10mM Tris-HCL, 75mM NaCl |
Grid | Details: Glow discharged carbon coated Cu/Rh 300 mesh Quantifoil R 1.2/1.3um grids. |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC Method: Blot for 1min before plunging with 5ul purified sample. |
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Electron microscopy
Microscope | OTHER |
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Date | Jul 17, 2014 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 84 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 84269 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | The XMIPP automatic picking routine was used to select particles. |
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CTF correction | Details: Each image |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: XMIPP3, EMAN2 / Number images used: 18346 |
Final two d classification | Number classes: 64 |