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- EMDB-45484: Transferrin Binding Protein A in complex with transferrin (iron b... -

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Basic information

Entry
Database: EMDB / ID: EMD-45484
TitleTransferrin Binding Protein A in complex with transferrin (iron bound in N lobe only)
Map dataTransferrin Binding Protein A in complex with transferrin (iron bound in N lobe only)
Sample
  • Complex: Transferrin binding protein A/Tf
    • Complex: TbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: Tf
      • Protein or peptide: Serotransferrin
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION
KeywordsMembrane protein / metal transporter / iron import / ton B-dependent transporter / TRANSPORT PROTEIN
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
Serotransferrin / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsDubey S / Noinaj N
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45484.png

Downloads & links

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Map

FileDownload / File: emd_45484.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTransferrin Binding Protein A in complex with transferrin (iron bound in N lobe only)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 250 pix.
= 269.5 Å		1.08 Å/pix.
x 250 pix.
= 269.5 Å		1.08 Å/pix.
x 250 pix.
= 269.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.178
Minimum - Maximum-0.45181447 - 0.732894
Average (Standard dev.)0.0020968365 (±0.026713723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 269.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_45484_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_45484_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transferrin binding protein A/Tf

EntireName: Transferrin binding protein A/Tf
Components
  • Complex: Transferrin binding protein A/Tf
    • Complex: TbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: Tf
      • Protein or peptide: Serotransferrin
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION

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Supramolecule #1: Transferrin binding protein A/Tf

SupramoleculeName: Transferrin binding protein A/Tf / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 80 kDa/nm

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Supramolecule #2: TbpA

SupramoleculeName: TbpA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)

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Supramolecule #3: Tf

SupramoleculeName: Tf / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serotransferrin

MacromoleculeName: Serotransferrin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.153906 KDa
SequenceString: MRLAVGALLV CAVLGLCLAV PDKTVRWCAV SEHEATKCQS FRDHMKSVIP SDGPSVACVK KASYLDCIRA IAANEADAVT LDAGLVYDA YLAPNNLKPV VAEFYGSKED PQTFYYAVAV VKKDSGFQMN QLRGKKSCHT GLGRSAGWNI PIGLLYCDLP E PRKPLEKA ...String:
MRLAVGALLV CAVLGLCLAV PDKTVRWCAV SEHEATKCQS FRDHMKSVIP SDGPSVACVK KASYLDCIRA IAANEADAVT LDAGLVYDA YLAPNNLKPV VAEFYGSKED PQTFYYAVAV VKKDSGFQMN QLRGKKSCHT GLGRSAGWNI PIGLLYCDLP E PRKPLEKA VANFFSGSCA PCADGTDFPQ LCQLCPGCGC STLNQYFGYS GAFKCLKDGA GDVAFVKHST IFENLANKAD RD QYELLCL DNTRKPVDEY KDCHLAQVPS HTVVARSMGG KEDLIWELLN QAQEHFGKDK SKEFQLFSSP HGKDLLFKDS AHG FLKVPP RMDAKMYLGY EYVTAIRNLR EGTCPEAPTD ECKPVKWCAL SHHERLKCDE WSVNSVGKIE CVSAETTEDC IAKI MNGEA DAMSLDGGFV YIAGKCGLVP VLAENYNKSD NCEDTPEAGY FAVAVVKKSA SDLTWDNLKG KKSCHTAVGR TAGWN IPMG LLYNKINHCR FDEFFSEGCA PGSKKDSSLC KLCMGSGLNL CEPNNKEGYY GYTGAFRCLV EKGDVAFVKH QTVPQN TGG KNPDPWAKNL NEKDYELLCL DGTRKPVEEY ANCHLARAPN HAVVTRKDKE ACVHKILRQQ QHLFGSNVTD CSGNFCL FR SETKDLLFRD DTVCLAKLHD RNTYEKYLGE EYVKAVGNLR KCSTSSLLEA CTFRRP

UniProtKB: Serotransferrin

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Macromolecule #2: Transferrin-binding protein A

MacromoleculeName: Transferrin-binding protein A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria) / Strain: MC58
Molecular weightTheoretical: 102.454594 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSNHHHHHHH HHHENLYFQG AMDIENVQAG QAQEKQLDTI QVKAKKQDTR RDNEVTGLGK LVKSSDTLSK EQVLNIRDLT RYDPGIAVV EQGRGASSGY SIRGMDKNRV SLTVDGVSQI QSYTAQAALG GTRTAGSSGA INEIEYENVK AVEISKGSNS V EQGSGALA ...String:
MSNHHHHHHH HHHENLYFQG AMDIENVQAG QAQEKQLDTI QVKAKKQDTR RDNEVTGLGK LVKSSDTLSK EQVLNIRDLT RYDPGIAVV EQGRGASSGY SIRGMDKNRV SLTVDGVSQI QSYTAQAALG GTRTAGSSGA INEIEYENVK AVEISKGSNS V EQGSGALA GSVAFQTKTA DDVIGEGRQW GIQSKTAYSG KNRGLTQSIA LAGRIGGAEA LLIHTGRRAG EIRAHEDAGR GV QSFNRLV PVEDSSNYAY FIVKEECKNG SYETCKANPK KDVVGKDERQ TVSTRDYTGP NRFLADPLSY ESRSWLFRPG FRF ENKRHY IGGILEHTQQ TFDTRDMTVP AFLTKAVFDA NKKQAGSLPG NGKYAGNHKY GGLFTNGENG ALVGAEYGTG VFYD ETHTK SRYGLEYVYT NADKDTWADY ARLSYDRQGV GLDNHFQQTH CSADGSDKYC RPSADKPFSY YKSDRVIYGE SHRLL QAAF KKSFDTAKIR HNLSVNLGFD RFGSNLRHQD YYYQHANRAY SSNTPPQNNG KKISPNGSET SPYWVTIGRG NVVTGQ ICR LGNNTYTDCT PRSINGKSYY AAVRDNVRLG RWADVGAGLR YDYRSTHSDD GSVSTGTHRT LSWNAGIVLK PTDWLDL TY RTSTGFRLPS FAEMYGWRAG VQSKAVKIDP EKSFNKEAGI VFKGDFGNLE ASWFNNAYRD LIVRGYEAQI KDGKEEAK G DPAYLNAQSA RITGINILGK IDWNGVWDKL PEGWYSTFAY NRVRVRDIKK RADRTDIQSH LFDAIQPSRY VVGLGYDQP EGKWGVNGML TYSKAKEITE LLGSRALLNG NSRNTKATAR RTRPWYIVDV SGYYTVKKHF TLRAGVYNLL NYRYVTWENV RQTAGGAVN QHKNVGVYNR YAAPGRNYTF SLEYKF

UniProtKB: Transferrin-binding protein A

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Macromolecule #3: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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

Concentration2.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.52 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: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3v89

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36642
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9cdq:
Transferrin Binding Protein A in complex with transferrin (iron bound in N lobe only)

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