+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20262 | |||||||||
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Title | Structure of YbtPQ importer | |||||||||
Map data | YbtPQ importer with substrate Ybt-Fe bound | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (strain UTI89 / UPEC) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 Å | |||||||||
Authors | Wang Z / Hu W / Zheng H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2020 Title: Pathogenic siderophore ABC importer YbtPQ adopts a surprising fold of exporter. Authors: Zhiming Wang / Wenxin Hu / Hongjin Zheng / Abstract: To fight for essential metal ions, human pathogens secrete virulence-associated siderophores and retake the metal-chelated siderophores through a subfamily of adenosine triphosphate (ATP)-binding ...To fight for essential metal ions, human pathogens secrete virulence-associated siderophores and retake the metal-chelated siderophores through a subfamily of adenosine triphosphate (ATP)-binding cassette (ABC) importer, whose molecular mechanisms are completely unknown. We have determined multiple structures of the yersiniabactin importer YbtPQ from uropathogenic (UPEC) at inward-open conformation in both and substrate-bound states by cryo-electron microscopy. YbtPQ does not adopt any known fold of ABC importers but surprisingly adopts the fold of type IV ABC exporters. To our knowledge, it is the first time an exporter fold of ABC importer has been reported. We have also observed two unique features in YbtPQ: unwinding of a transmembrane helix in YbtP upon substrate release and tightly associated nucleotide-binding domains without bound nucleotides. Together, our study suggests that siderophore ABC importers have a distinct transport mechanism and should be classified as a separate subfamily of ABC importers. | |||||||||
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_20262.map.gz | 9.2 MB | EMDB map data format | |
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Header (meta data) | emd-20262-v30.xml emd-20262.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | emd_20262.png | 149.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20262 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20262 | HTTPS FTP |
-Related structure data
Related structure data | 6p6iMC 6p6jC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20262.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | YbtPQ importer with substrate Ybt-Fe bound | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.864 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 : YbtPQ
Entire | Name: YbtPQ |
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Components |
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-Supramolecule #1: YbtPQ
Supramolecule | Name: YbtPQ / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (strain UTI89 / UPEC) (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: NOT APPLICABLE |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265627 |