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Yorodumi- PDB-8blw: Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta -
+Open data
-Basic information
Entry | Database: PDB / ID: 8blw | ||||||
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Title | Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Outer membrane / TonB-dependent transporter / vitamin B12 / lipoprotein | ||||||
Function / homology | Function and homology information siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
Authors | Silale, A. / Abellon-Ruiz, J. / van den Berg, B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B uptake in gut Bacteroides. Authors: Javier Abellon-Ruiz / Kalyanashis Jana / Augustinas Silale / Andrew M Frey / Arnaud Baslé / Matthias Trost / Ulrich Kleinekathöfer / Bert van den Berg / Abstract: Vitamin B (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition ...Vitamin B (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B outer membrane transporters together with a conserved array of surface-exposed B-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B with high affinities. Closing of the BtuG lid following B capture causes destabilisation of the bound B by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8blw.cif.gz | 256.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8blw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8blw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8blw_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8blw_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8blw_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 8blw_validation.cif.gz | 78.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/8blw ftp://data.pdbj.org/pub/pdb/validation_reports/bl/8blw | HTTPS FTP |
-Related structure data
Related structure data | 16114MC 8bmxC 8bmyC 8bmzC 8bn0C 8okvC 8p97C 8p98C 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: 78312.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria) References: UniProt: Q8A7N5 |
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#2: Protein | Mass: 73797.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 References: UniProt: Q8A7N4 |
#3: Sugar | ChemComp-GAL / |
Has ligand of interest | N |
-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: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.126 MDa / Experimental value: NO |
Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Source (recombinant) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Buffer solution | pH: 7.5 / Details: 10 mM HEPES-NaOH, 100 mM NaCl, 0.05% DDM |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.66 sec. / Electron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1924 |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50547 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.31 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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