+Open data
-Basic information
Entry | Database: PDB / ID: 8vsi | ||||||
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Title | Mechanistic Insights Revealed by YbtPQ in the Occluded State | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ABC importer / siderophore / occluded | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Hu, W. / Parkinson, C. / Zheng, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biomolecules / Year: 2024 Title: Mechanistic Insights Revealed by YbtPQ in the Occluded State. Authors: Wenxin Hu / Chance Parkinson / Hongjin Zheng / Abstract: Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of ...Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of "alternating access" like those exporters, cycling through inward-open, occluded, and outward-open conformations. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies on all the major conformations. To shed light on this, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic in the occluded conformation trapped by ADP-vanadate (ADP-Vi) at a 3.1 Å resolution determined by cryo-electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of the nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the "screwdriver" action at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vsi.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vsi.ent.gz | 164.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vsi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8vsi_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8vsi_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 8vsi_validation.cif.gz | 61.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/8vsi ftp://data.pdbj.org/pub/pdb/validation_reports/vs/8vsi | HTTPS FTP |
-Related structure data
Related structure data | 43498MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 66348.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: ybtP, A6592_10635, C3F40_00590, D4M65_13510, D4U49_03795, EIA08_14955, ERS139208_04188, FGG80_02235, HL563_00165, HL601_15305, HLV18_02815, NCTC9044_05702 Production host: Escherichia coli (E. coli) References: UniProt: A0A1D7Q186, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances | ||||
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#2: Protein | Mass: 66526.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: irp_2, NCTC11341_06313 / Production host: Escherichia coli (E. coli) References: UniProt: A0A376P7T7, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances | ||||
#3: Chemical | #4: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: YbtPQ / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340080 / Symmetry type: POINT | ||||||||||||||||||||||||
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