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Open data
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Basic information
Entry | Database: PDB / ID: 8p98 | ||||||
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Title | BtuB3G3 bound to cyanocobalamin with ordered EL8 | ||||||
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![]() | MEMBRANE PROTEIN / Cyanocobalamin / transporter / lipoprotein / complex | ||||||
Function / homology | ![]() Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
![]() | Silale, A. / Abellon-Ruiz, J. / van den Berg, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255 KB | Display | ![]() |
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PDB format | ![]() | 161 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 53.3 KB | Display | |
Data in CIF | ![]() | 75.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17575MC ![]() 8blwC ![]() 8bmxC ![]() 8bmyC ![]() 8bmzC ![]() 8bn0C ![]() 8okvC ![]() 8p97C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 81169.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: btuB_6 Production host: ![]() References: UniProt: A0A0P0F201 |
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#2: Protein | Mass: 41165.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q8A5Z1 |
#3: Chemical | ChemComp-CNC / |
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 |
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Sample preparation
Component | Name: Complex of TonB-dependent transporter BtuB3 with surface lipoprotein BtuG3 bound to cyanocobalamin (state 1) Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.122 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The protein complex was purified in lauryl maltose neopentyl glycol (LMNG). Prior to making grids, the sample was subjected to size exclusion chromatography without LMNG in the mobile phase ...Details: The protein complex was purified in lauryl maltose neopentyl glycol (LMNG). Prior to making grids, the sample was subjected to size exclusion chromatography without LMNG in the mobile phase to separate protein-LMNG complexes from free LMNG. | |||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 35.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9826 |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3311038 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66318 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.43 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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