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- EMDB-46743: Transferrin Binding Protein A in complex with transferrin binding... -

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Basic information

Entry
Database: EMDB / ID: EMD-46743
TitleTransferrin Binding Protein A in complex with transferrin binding protein B, transferrin and globular domain of TonB
Map data
Sample
  • Complex: Tbp/TbpB/Tf/TonB
    • Complex: TbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: Tf
      • Protein or peptide: Transferrin-binding protein B
    • Complex: TbpB
      • Protein or peptide: Serotransferrin
    • Complex: TonB
      • Protein or peptide: Protein TonB
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION
KeywordsTonB dependent Transporter / Iron Bound triple complex of Tbp-Tf system / Iron transporter / Tbp proteins / MEMBRANE PROTEIN / Ton Complex
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / energy transducer activity / siderophore transmembrane transport / iron chaperone activity / siderophore uptake transmembrane transporter activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / plasma membrane protein complex / endocytic vesicle ...ferric iron transmembrane transporter activity / energy transducer activity / siderophore transmembrane transport / iron chaperone activity / siderophore uptake transmembrane transporter activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / plasma membrane protein complex / 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 / Iron uptake and transport / ferrous iron binding / positive regulation of receptor-mediated endocytosis / recycling endosome / multicellular organismal-level iron ion homeostasis / transmembrane transport / 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 / protein transport / Clathrin-mediated endocytosis / antibacterial humoral response / 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 / Transferrin-binding protein B, N-lobe handle / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB/TolA, C-terminal / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain ...TonB-dependent lactoferrin/transferrin receptor / Transferrin-binding protein B, N-lobe handle / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / TonB/TolA, C-terminal / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / TbpB, N-lobe handle domain superfamily / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / 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 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Serotransferrin / Protein TonB / Transferrin-binding protein B / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria) / Homo sapiens (human) / Neisseria meningitidis serogroup B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDubey S / Noinaj N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
CitationJournal: To Be Published
Title: Transferrin Binding Protein A in complex with transferrin binding protein B, transferrin and globular domain of TonB
Authors: Dubey S / Noinaj N
History
DepositionAug 25, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46743.png

Downloads & links

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Map

FileDownload / File: emd_46743.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 460 pix.
= 441.14 Å		0.96 Å/pix.
x 460 pix.
= 441.14 Å		0.96 Å/pix.
x 460 pix.
= 441.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.385
Minimum - Maximum-1.3017503 - 2.6238832
Average (Standard dev.)0.00065786147 (±0.058938127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 441.13998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46743_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46743_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tbp/TbpB/Tf/TonB

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

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Supramolecule #1: Tbp/TbpB/Tf/TonB

SupramoleculeName: Tbp/TbpB/Tf/TonB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4
Molecular weightTheoretical: 12 KDa

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Supramolecule #2: TbpA

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

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Supramolecule #3: Tf

SupramoleculeName: Tf / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: TbpB

SupramoleculeName: TbpB / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 80 KDa

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Supramolecule #5: TonB

SupramoleculeName: TonB / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)

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Macromolecule #1: Transferrin-binding protein A

MacromoleculeName: Transferrin-binding protein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 102.506891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNHHHHHHH HHHENLYFQG AMDIENVQAG QAQEKQLDTI QVKAKKQKTR RDNEVTGLGK LVKSSDTLSK EQVLNIRDLT RYDPGIAVV EQGRGASSGY SIRGMDKNRV SLTVDGVSQI QSYTAQAALG GTRTAGSSGA INEIEYENVK AVEISKGSNS V EQGSGALA ...String:
MSNHHHHHHH HHHENLYFQG AMDIENVQAG QAQEKQLDTI QVKAKKQKTR 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 KKSFDAAKIR HNLSMNLGFD RFGSNMRHQD 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 NRMRVRDIKK RADRTDIQSH LFDAIQPSRY VVGLGYDQP EGKWGVNGML TYSKAKEITE LLGSRALLNG NSRNTKATAR RTRPWYIVDV SGYYTVKKHF TLRAGVYNLM NYRYVTWENV RQTAGGAVN QHKNVGVYNR YAAPGRNYTF SLEMKF

UniProtKB: Transferrin-binding protein A

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Macromolecule #2: Transferrin-binding protein B

MacromoleculeName: Transferrin-binding protein B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 75.381773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLGGGGSFDL DSVDTEAPRP APKYQDVFSE KPQAQKDQGG YGFAMRLKRR NWYPQAKEDE VKLDESDWEA TGLPDEPKEL PKRQKSVIE KVETDSDNNI YSSPYLKPSN HQNGNTGNGI NQPKNQAKDY ENFKYVYSGW FYKHAKREFN LKVEPKSAKN G DDGYIFYH ...String:
MLGGGGSFDL DSVDTEAPRP APKYQDVFSE KPQAQKDQGG YGFAMRLKRR NWYPQAKEDE VKLDESDWEA TGLPDEPKEL PKRQKSVIE KVETDSDNNI YSSPYLKPSN HQNGNTGNGI NQPKNQAKDY ENFKYVYSGW FYKHAKREFN LKVEPKSAKN G DDGYIFYH GKEPSRQLPA SGKITYKGVW HFATDTKKGQ KFREIIQPSK SQGDRYSGFS GDDGEEYSNK NKSTLTDGQE GY GFTSNLE VDFHNKKLTG KLIRNNANTD NNQATTTQYY SLEAQVTGNR FNGKATATDK PQQNSETKEH PFVSDSSSLS GGF FGPQGE ELGFRFLSDD QKVAVVGSAK TKDKPANGNT AAASGGTDAA ASNGAAGTSS ENGKLTTVLD AVELKLGDKK VQKL DNFSN AAQLVVDGIM IPLLPEASES GNNQANQGTN GGTAFTRKFD HTPESDKKDA QAGTQTNGAQ TASNTAGDTN GKTKT YEVE VCCSNLNYLK YGMLTRKNSK SAMQAGESSS QADAKTEQVE QSMFLQGERT DEKEIPSEQN IVYRGSWYGY IANDKS TSW SGNASNATSG NRAEFTVNFA DKKITGTLTA DNRQEATFTI DGNIKDNGFE GTAKTAESGF DLDQSNTTRT PKAYITD AK VQGGFYGPKA EELGGWFAYP GDKQTKNATN ASGNSSATVV FGAKRQQPVQ

UniProtKB: Transferrin-binding protein B

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Macromolecule #3: Serotransferrin

MacromoleculeName: Serotransferrin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.04175 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 CTFRAA

UniProtKB: Serotransferrin

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Macromolecule #4: Protein TonB

MacromoleculeName: Protein TonB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 11.9503 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHDYDI PTTENLYFQG AMSKGNPLRA NGSIPRPAYP TLSMENDEQG TVVLSVLVSP GGHVESVKIV KSSGFSRLDN AARKAAQNG HFQANAWTEF KVPVKFELN

UniProtKB: Protein TonB

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Macromolecule #5: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 5 / 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 #6: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 6 / 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

BufferpH: 7.5
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: 65.81 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1751004
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3v8x

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92329
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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