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- PDB-9gbc: Bacteroides thetaiotaomicron siderophore transporter XusA in comp... -

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Basic information

Entry
Database: PDB / ID: 9gbc
TitleBacteroides thetaiotaomicron siderophore transporter XusA in complex with surface-exposed lipoprotein XusB
Components
  • DUF4374 domain-containing protein
  • TonB-linked outer membrane receptor
KeywordsMETAL TRANSPORT / Outer membrane / membrane protein complex / siderophore transport / iron piracy
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSilale, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: Structural basis of iron piracy by human gut Bacteroides
Authors: Silale, A. / Soo, Y.L. / Mark, H. / Basle, A. / van den Berg, B.
History
DepositionJul 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TonB-linked outer membrane receptor
B: DUF4374 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)140,9422
Polymers140,9422
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein TonB-linked outer membrane receptor


Mass: 89255.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A621
#2: Protein DUF4374 domain-containing protein


Mass: 51686.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A C-terminal His6-tag coding sequence was fused to the xusB gene on the B. thetaiotaomicron chromosome.
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_2064
Production host: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
References: UniProt: Q8A622
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron
Type: COMPLEX
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.
Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
110 mMHEPES-NaOH1
2100 mMsodium chloride1
30.03 %dodecyl maltoside1
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: 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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40.83 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6645
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1110843
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76969 / Symmetry type: POINT
Atomic model buildingB value: 57.2 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: other
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028826
ELECTRON MICROSCOPYf_angle_d0.53511968
ELECTRON MICROSCOPYf_dihedral_angle_d4.5791214
ELECTRON MICROSCOPYf_chiral_restr0.0451276
ELECTRON MICROSCOPYf_plane_restr0.0061556

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