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Yorodumi- EMDB-16114: Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16114 | |||||||||
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Title | Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta | |||||||||
Map data | Sharpened with bfactor=-50 | |||||||||
Sample |
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Keywords | Outer membrane / TonB-dependent transporter / vitamin B12 / lipoprotein / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Silale A / Abellon-Ruiz J / van den Berg B | |||||||||
Funding support | United Kingdom, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16114.map.gz | 110.9 MB | EMDB map data format | |
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Header (meta data) | emd-16114-v30.xml emd-16114.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16114_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_16114.png | 65.1 KB | ||
Masks | emd_16114_msk_1.map | 216 MB | Mask map | |
Others | emd_16114_additional_1.map.gz emd_16114_half_map_1.map.gz emd_16114_half_map_2.map.gz | 108.3 MB 200.4 MB 200.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16114 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16114 | HTTPS FTP |
-Validation report
Summary document | emd_16114_validation.pdf.gz | 979.4 KB | Display | EMDB validaton report |
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Full document | emd_16114_full_validation.pdf.gz | 979 KB | Display | |
Data in XML | emd_16114_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_16114_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16114 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16114 | HTTPS FTP |
-Related structure data
Related structure data | 8blwMC 8bmxC 8bmyC 8bmzC 8bn0C 8okvC 8p97C 8p98C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16114.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened with bfactor=-50 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16114_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_16114_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_16114_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_16114_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein...
Entire | Name: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1 |
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Components |
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-Supramolecule #1: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein...
Supramolecule | Name: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Molecular weight | Theoretical: 126 KDa |
-Macromolecule #1: Vitamin B12 transporter BtuB1
Macromolecule | Name: Vitamin B12 transporter BtuB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Molecular weight | Theoretical: 78.31275 KDa |
Recombinant expression | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Sequence | String: MRRNTFIKKM SVLLCCQALS LSLFAQQQKV DTAHIYSIPE IMVSDPYQTR EVRSASPLQV FNKEELKNLQ ALQVSDAVKH FAGVTVKDY GGIGGLKTVS IRSLGAQHTA VSYDGITVSD CQTGQVDIGR FSLNNVDRLS LNNGQSDNIF QPARFFASAG I LNIQTLTP ...String: MRRNTFIKKM SVLLCCQALS LSLFAQQQKV DTAHIYSIPE IMVSDPYQTR EVRSASPLQV FNKEELKNLQ ALQVSDAVKH FAGVTVKDY GGIGGLKTVS IRSLGAQHTA VSYDGITVSD CQTGQVDIGR FSLNNVDRLS LNNGQSDNIF QPARFFASAG I LNIQTLTP HFKEDKPTNI AAEFKTGSWG LVNPSLFLEQ QLNKKWSMTA NGEWMSSDGH YPFTLRYGND ADVQVSKEKR RN TDVENLR AEISAFANLS DKEQWRLKAY YYQSSRGLPN ATTLYYDFSR QNLRDKNTFI QSQYKKEFSR KWVFQTSAKW NWS YQNYQD PDALTSVGGT DNSYYQQEYY LSASALYRIW NNLSFSLSTD GSINTMNANL QNFVSPTRYS WLTAFAGKYV NEWV TLSAS ALATVINEKA KNGGNAGNHR KLSPNVSISL KPFHNEELRF RFFYKDIFRL PSFNDLYYDK AGNINLKPES ATQYN IGIT YSKAINNFIP YLSATVDAYH NKVTDKIVAT PTKNLFIWSM VNLGKVDIKG IDATASLSLQ PLDKLRINLS GNYTYQ RAL DVTNSNPNSP EGKVYKHQIA YTPRVSASGQ AGIETPWLNL SYSFLFSGKR YMLGQNISDN RLDSYSDHSI SAYRDFK IQ KVTASLNLEV LNLMNRNYEI VKNFPMPGRS VRVTIGVRYG GGHHHHHH UniProtKB: Vitamin B12 receptor, outer membrane |
-Macromolecule #2: YncE family protein
Macromolecule | Name: YncE family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 |
Molecular weight | Theoretical: 73.797047 KDa |
Sequence | String: MQKGLLYNML LRLGKYFFLF PLFFIACDDL EDKPSIVPES NGDVFETGTA EMYILSEGLF NQNNSSLARY SFNRQRCTNN YFSANNQRG LGDTANDIAI YGNKIYVVVN VSSTVEVIDF PTGKSIRQIS MLRDNGSSRQ PRAIAFDKDK AYICSYDGTV A RIDTTSLE ...String: MQKGLLYNML LRLGKYFFLF PLFFIACDDL EDKPSIVPES NGDVFETGTA EMYILSEGLF NQNNSSLARY SFNRQRCTNN YFSANNQRG LGDTANDIAI YGNKIYVVVN VSSTVEVIDF PTGKSIRQIS MLRDNGSSRQ PRAIAFDKDK AYICSYDGTV A RIDTTSLE IEEIVTVGRN AEDICVQNGK LYVSNSGGLD YSGPGVDTTV SVIDITTFKE TKKIEVGPNP GKILPGLEEA VY VVTRGTD IEAGDYHLVK IDSRTDAVAI TYDEKVLSFA IDGPIAYLYT YDYQTKDSAI KVFDLNAGTV IRDNFITDGT AIQ TPFSIQ LNPFSGNIYI TEAYNYTVKG DVLCFNQQGQ LQYRLNDIGL NPNTVVFSDK ASQNEAGDTP EDPNAPSAFA NKVF EYIPA PGQFINTTTS AYEDGFSAGQ VLEHATEKLK KKSVISLGGF GGTITVGFHQ SIRNSKGEYD FRILGNASYN QNTGT GALG GSAEPGIVLV SKDENGNGLP DDEWYELAGS EYGKDTETRN YEITYYRPQP ANGDVRWTDN QGGEGFVYRN SYHQQD SYY PNWIEEDEIT FRGTRLKDNA INEGGTWVGY CYPWGYADNH PNRSEFSQFK IDWAVDQNGN HVELDKIDFV KIYTAVN QN VGWMGEISTE VMTVEDLHFE N UniProtKB: YncE family protein |
-Macromolecule #3: beta-D-galactopyranose
Macromolecule | Name: beta-D-galactopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: GAL |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-GAL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 10 mM HEPES-NaOH, 100 mM NaCl, 0.05% DDM |
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1924 / Average exposure time: 4.66 sec. / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 50 |
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Output model | PDB-8blw: |