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- PDB-9cdq: Transferrin Binding Protein A in complex with transferrin (iron b... -

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Basic information

Entry
Database: PDB / ID: 9cdq
TitleTransferrin Binding Protein A in complex with transferrin (iron bound in N lobe only)
Components
  • Serotransferrin
  • Transferrin-binding protein A
KeywordsTRANSPORT PROTEIN / Membrane protein / metal transporter / iron import / ton B-dependent transporter
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / siderophore transmembrane transport / iron chaperone activity / siderophore uptake transmembrane transporter activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding ...ferric iron transmembrane transporter activity / siderophore transmembrane transport / iron chaperone activity / siderophore uptake transmembrane transporter activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / osteoclast differentiation / basal plasma membrane / Post-translational protein phosphorylation / cell outer membrane / iron ion transport / clathrin-coated endocytic vesicle membrane / regulation of protein stability / HFE-transferrin receptor complex / cellular response to iron ion / ferrous iron binding / Iron uptake and transport / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / recycling endosome / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / antibacterial humoral response / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / intracellular iron ion homeostasis / transmembrane transporter binding / early endosome / cell surface receptor signaling pathway / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / cell surface / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
TonB-dependent lactoferrin/transferrin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / Serotransferrin, mammalian / TonB box, conserved site / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. ...TonB-dependent lactoferrin/transferrin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB-dependent receptor (TBDR) proteins signature 1. / Serotransferrin, mammalian / TonB box, conserved site / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / 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 / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
BICARBONATE ION / : / Serotransferrin / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsDubey, S. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
CitationJournal: Sci Adv / Year: 2026
Title: Structural insights into the mechanism underpinning iron piracy in pathogenic .
Authors: Shubham Dubey / Julie Stoudenmire / Gabriel Bury / Lixinhao Yang / Zixing Fan / Peihang Li / Gauree Wadhwa / Yulia Pushkar / James C Gumbart / Cynthia Nau Cornelissen / Nicholas Noinaj /
Abstract: The pathogenesis of hinges on the surface proteins TbpA and TbpB, which orchestrate the acquisition of iron from transferrin. TbpB selectively captures iron-loaded transferrin and delivers it to ...The pathogenesis of hinges on the surface proteins TbpA and TbpB, which orchestrate the acquisition of iron from transferrin. TbpB selectively captures iron-loaded transferrin and delivers it to TbpA for iron import. We report a series of cryo-electron microscopy structures of trapped intermediates along the iron acquisition pathway. These structural studies are supported by pulldowns, electron paramagnetic resonance studies, molecular dynamics simulations, and studies in , which show that TbpA mechanically opens the C-lobe of transferrin, triggering iron release. Once iron is removed, TbpB dissociates and undergoes large subunit rearrangements with its C-lobe rebinding at a different interface on transferrin. TonB binding expands the barrel of TbpA, helping displace the plug to open a path for iron import. This also disrupts the interaction of the plug loop with the C1 domain of transferrin, leading to the dissociation of the spent transferrin. Together, our study provides a more complete understanding of metal acquisition systems in and other Gram-negative bacteria.
History
DepositionJun 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Serotransferrin
A: Transferrin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7254
Polymers179,6092
Non-polymers1172
Water00
1


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

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Components

#1: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 77153.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787
#2: Protein Transferrin-binding protein A / TbpA / Transferrin-binding protein 1


Mass: 102454.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: tbp1, tbpA, NMB0461
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9K0U9
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Transferrin binding protein A/TfCOMPLEX#1-#20RECOMBINANT
2TbpACOMPLEX#21RECOMBINANT
3TfCOMPLEX#11NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.1 MDaNO
2180 kDa/nmNO
42
53
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Neisseria meningitidis serogroup B (bacteria)491
32Neisseria meningitidis serogroup B (bacteria)491
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
32Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
43Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 7.8
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 53.52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36642 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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