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- EMDB-51210: Bacteroides thetaiotaomicron siderophore transporter XusA in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-51210
TitleBacteroides thetaiotaomicron siderophore transporter XusA in complex with surface-exposed lipoprotein XusB
Map dataUnsharpened map
Sample
  • Complex: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron
    • Protein or peptide: TonB-linked outer membrane receptor
    • Protein or peptide: DUF4374 domain-containing protein
  • Ligand: water
KeywordsOuter membrane / membrane protein complex / siderophore transport / iron piracy / METAL TRANSPORT
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane
Similarity search - Function
Protein of unknown function DUF4374 / Domain of unknown function (DUF4374) / CarboxypepD_reg-like domain / Carboxypeptidase-like, regulatory domain superfamily / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
TonB-linked outer membrane receptor / DUF4374 domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSilale A / van den Berg B
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis of iron piracy by human gut .
Authors: Augustinas Silale / Yung Li Soo / Hannah Mark / Rachel N Motz / Arnaud Baslé / Elizabeth M Nolan / Bert van den Berg /
Abstract: Iron is an essential element that can be growth-limiting in microbial communities, particularly those present within host organisms. To acquire iron, many bacteria secrete siderophores, secondary ...Iron is an essential element that can be growth-limiting in microbial communities, particularly those present within host organisms. To acquire iron, many bacteria secrete siderophores, secondary metabolites that chelate ferric iron. These iron chelates can be transported back into the cell via TonB-dependent transporters in the outer membrane, followed by intracellular liberation of the iron. Pathogenic and produce siderophores during gut infection. In response to iron starvation, the human gut symbiont upregulates an iron piracy system, XusABC, which steals iron-bound siderophores from the invading pathogens. Here, we investigated the molecular details of xenosiderophore uptake across the outer membrane by the XusAB complex. Our crystal and cryogenic electron microscopy structures explain how the XusB lipoprotein recognises iron-bound xenosiderophores and passes them on to the XusA TonB-dependent transporter. Moreover, we show that Xus homologues can transport a variety of siderophores with different iron-chelating functional groups.
History
DepositionJul 30, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51210.png

Downloads & links

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Map

FileDownload / File: emd_51210.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 480 pix.
= 355.2 Å		0.74 Å/pix.
x 480 pix.
= 355.2 Å		0.74 Å/pix.
x 480 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0425
Minimum - Maximum-0.10909388 - 0.23805225
Average (Standard dev.)0.0000049040127 (±0.004484953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51210_msk_1.map
Projections & Slices
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Additional map: Sharpened map

Fileemd_51210_additional_1.map
AnnotationSharpened map
Projections & Slices
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Half map: Half map 1

Fileemd_51210_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_51210_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : Complex of TonB-dependent transporter XusA and surface-exposed li...

EntireName: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron
Components
  • Complex: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron
    • Protein or peptide: TonB-linked outer membrane receptor
    • Protein or peptide: DUF4374 domain-containing protein
  • Ligand: water

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Supramolecule #1: Complex of TonB-dependent transporter XusA and surface-exposed li...

SupramoleculeName: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: XusB was tagged with an affinity tag on the chromosome. The tag was used to pull down the XusAB complex at native expression levels.
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: TonB-linked outer membrane receptor

MacromoleculeName: TonB-linked outer membrane receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 89.255508 KDa
SequenceString: MINKSFLVFL AFLFSVSAFS QHGRSGGMIS GRVISTVEKE VVDFATVYLK GTNRGATTDE KGLYHLKAAA GDYTLVVSAI GYTTVEKKV TLKAGERIRV NVTIAPQVTE LNEVVVSTSA VSRVNKSAFN AVAIDAKGLH NSTQNLSDAL AKVPGLKLRE A GGVGSDMI ...String:
MINKSFLVFL AFLFSVSAFS QHGRSGGMIS GRVISTVEKE VVDFATVYLK GTNRGATTDE KGLYHLKAAA GDYTLVVSAI GYTTVEKKV TLKAGERIRV NVTIAPQVTE LNEVVVSTSA VSRVNKSAFN AVAIDAKGLH NSTQNLSDAL AKVPGLKLRE A GGVGSDMI LSLDGFSGKH VKLFIDGVPQ EGVGSSFGLN NIPINFADRI EVYRGVVPVG FGTDALGGVI NIVTNKNRKN WF LDASYSY GSFNTHKSYV NFGQTFKNGL TYEINAFQNY SDNSYYVDTP VEEFYEGGGS AINTDKVEHV KRFHDNYHNE AVV GKVGLV DKKWADRLMI GLTYSRMYKE IQTGVVQKVV FGEKYRKGNS LMPSLEYRKR NLFVRNLDVA FTANYNRNFT NNVD TATYR FNWLGEKTSL KGRKGEQSYQ DMKSDNDNWN ATFTANYHIG TAHTFVLNHV LNTFHRENHN SVSVDESNAI AKVTR KNIT GFSYRLMPSE HWNLSVFGKY YNQYNAGPVS ASTSGTSNYV RLTNNVSSVG YGAAGTYFIL SGLQAKLSYE KAYRLP TNE ELFGDEDLEL GKIGLNPEKS DNLNFNLSYN RQLGKHGLYV ETGLIYRNTS DYIYRSIETT SNRSYGSYSN YGSVETK GY HISARYNYSC WVSIGGNFTQ MDVRDNVEKT QTGQESLTYG ARMPNLPYRF ANSDISFFWR NLWKKGNTLT VTYDNMYV H GFPLYSEALG AVETKDIVPT QFSHNLGITY SLKNGRYNVS FECKNFTDEK LYDNFSLQKA GRAFYGKVRV YFGGN

UniProtKB: TonB-linked outer membrane receptor

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Macromolecule #2: DUF4374 domain-containing protein

MacromoleculeName: DUF4374 domain-containing protein / type: protein_or_peptide / ID: 2
Details: A C-terminal His6-tag coding sequence was fused to the xusB gene on the B. thetaiotaomicron chromosome.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 51.686082 KDa
Recombinant expressionOrganism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
SequenceString: MKKNFLMWSF AMALLTGTLC TSCDETEGAV APEETQSVQK GIAITYLHVT DQIMKNRDVI RGENFLGNGE YVTFAGILEA NNKIYTAPI PMGLSVYGSA FEDGKWVKYP ELVKTEDGGS NSSSYEKGEL QWTQYPNEAW VAIYNDENFN NPTLIRTDKI S YACGRMRS ...String:
MKKNFLMWSF AMALLTGTLC TSCDETEGAV APEETQSVQK GIAITYLHVT DQIMKNRDVI RGENFLGNGE YVTFAGILEA NNKIYTAPI PMGLSVYGSA FEDGKWVKYP ELVKTEDGGS NSSSYEKGEL QWTQYPNEAW VAIYNDENFN NPTLIRTDKI S YACGRMRS QYYQTIWAAD NGDVYVFSPS YAKIMDADVQ KTNLPAGVVR IKAGATDFDS YYCNLEELSG GKSFLRCWHI TG DYFLLQM YTGEINSRGT GATRMAVFKA TGNGDKGELY YVDGLPEPDR ISSFSGTPFC ENGVAYVGVI PITADGETNH PAI YKIDPV THTATKGLTV NATGITAIGR LAKDSHSTYV VSATVTSANS TANYLLATST LESGSVTPGN NNGFETATGT AWIF YKDQY LYRLQYNQGN EGVTTAYELN TNGGIAKRSN EYTITRFTTY GIFGENIISS SAVDATFTDH HHHHH

UniProtKB: DUF4374 domain-containing protein

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 120 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration7 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES-NaOH
100.0 mMsodium chloride
0.03 %dodecyl maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 6645 / Average electron dose: 40.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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

Particle selectionNumber selected: 1110843
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The initial model was generated from curated particle images using cryoSPARC's ab initio reconstruction job.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76969
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Details: The final refinement step was cryoSPARC's local refinement.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 57.2
Output model

PDB-9gbc:
Bacteroides thetaiotaomicron siderophore transporter XusA in complex with surface-exposed lipoprotein XusB

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