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Yorodumi- EMDB-22881: Cryo-EM structure of enteropathogenic Escherichia colitype III se... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22881 | |||||||||
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Title | Cryo-EM structure of enteropathogenic Escherichia colitype III secretion system EspA filament | |||||||||
Map data | Cryo-EM structure of enteropathogenic Escherichia coli type III secretion system EspA filament | |||||||||
Sample |
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Keywords | type III secretion system (T3SS) / EspA filament / Helical reconstruction / PROTEIN FIBRIL | |||||||||
Function / homology | EspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Translocon EspA Function and homology information | |||||||||
Biological species | Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Zheng W / Ilangovan A / Costa TRD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Cryoelectron-microscopy structure of the enteropathogenic type III secretion system EspA filament. Authors: Weili Zheng / Alejandro Peña / Aravindan Ilangovan / Yasaman Naemi Baghshomali / Gad Frankel / Edward H Egelman / Tiago R D Costa / Abstract: Enteropathogenic (EPEC) and enterohemorrhagic (EHEC) utilize a macromolecular type III secretion system (T3SS) to inject effector proteins into eukaryotic cells. This apparatus spans the inner and ...Enteropathogenic (EPEC) and enterohemorrhagic (EHEC) utilize a macromolecular type III secretion system (T3SS) to inject effector proteins into eukaryotic cells. This apparatus spans the inner and outer bacterial membranes and includes a helical needle protruding into the extracellular space. Thus far observed only in EPEC and EHEC and not found in other pathogenic Gram-negative bacteria that have a T3SS is an additional helical filament made by the EspA protein that forms a long extension to the needle, mediating both attachment to eukaryotic cells and transport of effector proteins through the intestinal mucus layer. Here, we present the structure of the EspA filament from EPEC at 3.4 Å resolution. The structure reveals that the EspA filament is a right-handed 1-start helical assembly with a conserved lumen architecture with respect to the needle to ensure the seamless transport of unfolded cargos en route to the target cell. This functional conservation is despite the fact that there is little apparent overall conservation at the level of sequence or structure with the needle. We also unveil the molecular details of the immunodominant EspA epitope that can now be exploited for the rational design of epitope display systems. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22881.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-22881-v30.xml emd-22881.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_22881.png | 253.4 KB | ||
Filedesc metadata | emd-22881.cif.gz | 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22881 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22881 | HTTPS FTP |
-Validation report
Summary document | emd_22881_validation.pdf.gz | 621.1 KB | Display | EMDB validaton report |
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Full document | emd_22881_full_validation.pdf.gz | 620.7 KB | Display | |
Data in XML | emd_22881_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_22881_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22881 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22881 | HTTPS FTP |
-Related structure data
Related structure data | 7khwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22881.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of enteropathogenic Escherichia coli type III secretion system EspA filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : EspA filament
Entire | Name: EspA filament |
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Components |
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-Supramolecule #1: EspA filament
Supramolecule | Name: EspA filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC |
-Macromolecule #1: Translocon EspA
Macromolecule | Name: Translocon EspA / type: protein_or_peptide / ID: 1 / Number of copies: 50 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC |
Molecular weight | Theoretical: 20.482811 KDa |
Sequence | String: MDTSTTASVA SANASTSTSM AYDLGSMSKD DVIDLFNKLG VFQAAILMFA YMYQAQSDLS IAKFADMNEA SKESTTAQKM ANLVDAKIA DVQSSSDKNA KAQLPDEVIS YINDPRNDIT ISGIDNINAQ LGAGDLQTVK AAISAKANNL TTTVNNSQLE I QQMSNTLN ...String: MDTSTTASVA SANASTSTSM AYDLGSMSKD DVIDLFNKLG VFQAAILMFA YMYQAQSDLS IAKFADMNEA SKESTTAQKM ANLVDAKIA DVQSSSDKNA KAQLPDEVIS YINDPRNDIT ISGIDNINAQ LGAGDLQTVK AAISAKANNL TTTVNNSQLE I QQMSNTLN LLTSARSDMQ SLQYRTISGI SLGK UniProtKB: Translocon EspA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.4 Å Applied symmetry - Helical parameters - Δ&Phi: 64.3 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 159460 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION |