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Yorodumi- PDB-8bmy: Bacteroides thetaiotaomicron surface lipoprotein bound to cyanoco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bmy | ||||||
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Title | Bacteroides thetaiotaomicron surface lipoprotein bound to cyanocobalamin | ||||||
Components | Putative surface layer protein | ||||||
Keywords | MEMBRANE PROTEIN / beta propeller surface protein B12 binding protein | ||||||
Function / homology | Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / CYANOCOBALAMIN / Surface layer protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Abellon-Ruiz, J. / Jana, K. / Silale, A. / Basle, A. / Kleinekathofer, U. / 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 | 8bmy.cif.gz | 528.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bmy.ent.gz | 424.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/8bmy ftp://data.pdbj.org/pub/pdb/validation_reports/bm/8bmy | HTTPS FTP |
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-Related structure data
Related structure data | 8blwC 8bmxC 8bmzC 8bn0C 8okvC 8p97C 8p98C 3dsmS S: Starting model for refinement 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 40 - 373 / Label seq-ID: 9 - 342
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 39951.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 Gene: BT_1954 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6D0 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium sulphate, 0.1M Tris pH 8.5, 1.26 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96858 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.72→59.08 Å / Num. obs: 97918 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.099 / Rrim(I) all: 0.147 / Net I/σ(I): 6 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DSM Resolution: 1.72→55.072 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.178 / SU B: 5.915 / SU ML: 0.083 / Average fsc free: 0.9091 / Average fsc work: 0.9235 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.103 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.783 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→55.072 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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