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- EMDB-45747: Transferrin Binding Protein A in complex with transferrin binding... -

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Basic information

Entry
Database: EMDB / ID: EMD-45747
TitleTransferrin Binding Protein A in complex with transferrin binding protein B and transferrin (iron bound in both lobes of Tf)
Map data
Sample
  • Complex: Tbp/TbpB/Tf (triple complex-iron bound)
    • Complex: TbpA
      • Protein or peptide: Transferrin-binding protein A
    • Complex: Tf
      • Protein or peptide: Transferrin
    • Complex: TbpB
      • Protein or peptide: Transferrin-binding protein B
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION
KeywordsTonB dependent Transporter / Iron Bound triple complex of Tbp-Tf system / Iron transporter / Tbp proteins / MEMBRANE 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 / Iron uptake and transport / ferrous iron binding / positive regulation of receptor-mediated endocytosis / recycling endosome / multicellular organismal-level iron ion homeostasis / 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 / 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-dependent haemoglobin/transferrin/lactoferrin receptor / 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 lactoferrin/transferrin receptor / Transferrin-binding protein B, N-lobe handle / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / 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 / Transferrin-binding protein B / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 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 and transferrin (iron bound in both lobes of Tf)
Authors: Dubey S / Noinaj N
History
DepositionJul 15, 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_45747.png

Downloads & links

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Map

FileDownload / File: emd_45747.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.8412955 - 1.4095545
Average (Standard dev.)0.0047899773 (±0.0454094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45747_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_45747_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 (triple complex-iron bound)

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

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Supramolecule #1: Tbp/TbpB/Tf (triple complex-iron bound)

SupramoleculeName: Tbp/TbpB/Tf (triple complex-iron bound) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3

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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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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 (bacteria)
Molecular weightTheoretical: 102.568977 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 KKSFDTAKIR HNLSMNLGFD RFGSNMRHQD YYYQHANRAY SSNTPPQNNG KKISPNGSET SPYWVTIGRG NVVTGQ ICR LGNNTYTDCT PRSINGKSYY AAVRDNMRLG 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

MacromoleculeName: Transferrin / type: protein_or_peptide / ID: 2 / 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 #3: Transferrin-binding protein B

MacromoleculeName: Transferrin-binding protein B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 75.684117 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMACLGGGG SFDLDSVDTE APRPAPKYQD VFSEKPQAQK DQGGYGFAMR LKRRNWYPQA KEDEVKLDES DWEATGLPDE PKELPKRQK SVIEKVETDS DNNIYSSPYL KPSNHQNGNT GNGINQPKNQ AKDYENFKYV YSGWFYKHAK REFNLKVEPK S AKNGDDGY ...String:
GAMACLGGGG SFDLDSVDTE APRPAPKYQD VFSEKPQAQK DQGGYGFAMR LKRRNWYPQA KEDEVKLDES DWEATGLPDE PKELPKRQK SVIEKVETDS DNNIYSSPYL KPSNHQNGNT GNGINQPKNQ AKDYENFKYV YSGWFYKHAK REFNLKVEPK S AKNGDDGY IFYHGKEPSR QLPASGKITY KGVWHFATDT KKGQKFREII QPSKSQGDRY SGFSGDDGEE YSNKNKSTLT DG QEGYGFT SNLEVDFHNK KLTGKLIRNN ANTDNNQATT TQYYSLEAQV TGNRFNGKAT ATDKPQQNSE TKEHPFVSDS SSL SGGFFG PQGEELGFRF LSDDQKVAVV GSAKTKDKPA NGNTAAASGG TDAAASNGAA GTSSENGKLT TVLDAVELKL GDKK VQKLD NFSNAAQLVV DGIMIPLLPE ASESGNNQAN QGTNGGTAFT RKFDHTPESD KKDAQAGTQT NGAQTASNTA GDTNG KTKT YEVEVCCSNL NYLKYGMLTR KNSKSAMQAG ESSSQADAKT EQVEQSMFLQ GERTDEKEIP SEQNIVYRGS WYGYIA NDK STSWSGNASN ATSGNRAEFT VNFADKKITG TLTADNRQEA TFTIDGNIKD NGFEGTAKTA ESGFDLDQSN TTRTPKA YI TDAKVQGGFY GPKAEELGGW FAYPGDKQTK NATNASGNSS ATVVFGAKRQ QPVQ

UniProtKB: Transferrin-binding protein B

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Macromolecule #4: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 2 / 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

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

3v8x

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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