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Yorodumi- EMDB-40194: The Type 9 Secretion System Extended Translocon - SprA-PorV-PPI-R... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40194 | |||||||||||||||||||||
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Title | The Type 9 Secretion System Extended Translocon - SprA-PorV-PPI-RemZ-SkpA-SprE complex | |||||||||||||||||||||
Map data | Composite volume used for refinement of coordinates created from EMD-29911 and EMD-40085 the associated consensus volume is EMD-40086 | |||||||||||||||||||||
Sample |
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Keywords | T9SS / Type IX Secretion System Translocon / Protein Secretion PorV - SprA - PPI - RemZ Complex / MEMBRANE PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information protein insertion into membrane from inner side / protein maturation by protein folding / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / outer membrane-bounded periplasmic space / protein stabilization Similarity search - Function | |||||||||||||||||||||
Biological species | Flavobacterium johnsoniae UW101 (bacteria) / Flavobacterium johnsoniae (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||||||||||||||
Authors | Deme JC / Lea SM | |||||||||||||||||||||
Funding support | United Kingdom, European Union, United States, 6 items
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Citation | Journal: Nat Microbiol / Year: 2024 Title: The Type 9 Secretion System caught in the act of transport Authors: Lauber F / Deme JC / Liu X / Kjaer A / Miller HL / Alcock F / Lea SM / Berks BC | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40194.map.gz | 42.3 MB | EMDB map data format | |
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Header (meta data) | emd-40194-v30.xml emd-40194.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
Images | emd_40194.png | 47 KB | ||
Filedesc metadata | emd-40194.cif.gz | 9.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40194 | HTTPS FTP |
-Validation report
Summary document | emd_40194_validation.pdf.gz | 390.7 KB | Display | EMDB validaton report |
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Full document | emd_40194_full_validation.pdf.gz | 390.3 KB | Display | |
Data in XML | emd_40194_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_40194_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40194 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40194 | HTTPS FTP |
-Related structure data
Related structure data | 8gl8MC 8gl6C 8gljC 8glkC 8glmC 8glnC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40194.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite volume used for refinement of coordinates created from EMD-29911 and EMD-40085 the associated consensus volume is EMD-40086 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Type 9 Secretion System Extended Translocon
+Supramolecule #1: Type 9 Secretion System Extended Translocon
+Macromolecule #1: Protein involved in gliding motility SprA
+Macromolecule #2: Peptidyl-prolyl cis-trans isomerase
+Macromolecule #3: Type IX secretion system protein PorV domain-containing protein
+Macromolecule #4: RemZ
+Macromolecule #5: Periplasmic chaperone for outer membrane proteins Skp
+Macromolecule #6: SprE
+Macromolecule #7: Lauryl Maltose Neopentyl Glycol
+Macromolecule #8: alpha-D-mannopyranose
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 546490 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |