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- EMDB-16114: Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta -

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Basic information

Entry
Database: EMDB / ID: EMD-16114
TitleVitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta
Map dataSharpened with bfactor=-50
Sample
  • Complex: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1
    • Protein or peptide: Vitamin B12 transporter BtuB1
    • Protein or peptide: YncE family protein
  • Ligand: beta-D-galactopyranose
KeywordsOuter 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
Quinoprotein amine dehydrogenase, beta chain-like / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / 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
YncE family protein / Vitamin B12 receptor, outer membrane
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsSilale A / Abellon-Ruiz J / van den Berg B
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: 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
DepositionNov 10, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16114.png

Downloads & links

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Map

FileDownload / File: emd_16114.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened with bfactor=-50
Voxel sizeX=Y=Z: 0.91 Å
Density
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.57086 - 1.0781782
Average (Standard dev.)0.0005462107 (±0.018556185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 349.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16114_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_16114_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half map A

Fileemd_16114_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_16114_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Sample components

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Entire : Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein...

EntireName: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1
Components
  • Complex: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1
    • Protein or peptide: Vitamin B12 transporter BtuB1
    • Protein or peptide: YncE family protein
  • Ligand: beta-D-galactopyranose

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Supramolecule #1: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein...

SupramoleculeName: Complex of B. theta vitamin B12 transporter BtuB1 and lipoprotein BtuG1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 126 KDa

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Macromolecule #1: Vitamin B12 transporter BtuB1

MacromoleculeName: Vitamin B12 transporter BtuB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 78.31275 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: 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

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Macromolecule #2: YncE family protein

MacromoleculeName: YncE family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Molecular weightTheoretical: 73.797047 KDa
SequenceString: 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

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Macromolecule #3: beta-D-galactopyranose

MacromoleculeName: beta-D-galactopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: GAL
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GAL:
beta-D-galactopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 10 mM HEPES-NaOH, 100 mM NaCl, 0.05% DDM
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 50
Output model

PDB-8blw:
Vitamin B12 transporter BtuB1 with lipoprotein BtuG1 from B. theta

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