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- EMDB-71436: NmTbpB and Tf protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-71436
TitleNmTbpB and Tf protein complex
Map data
Sample
  • Complex: Transferrin Binding protein B in complex with transferrin
    • Complex: Tf
      • Protein or peptide: Transferrin
    • Complex: TbpB
      • Protein or peptide: Transferrin-binding protein B
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION
KeywordsLipoprotein / Transferrin / Iron import / MEMBRANE PROTEIN
Function / homology
Function and homology information


iron chaperone 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 ...iron chaperone 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 / recycling endosome / positive regulation of receptor-mediated endocytosis / 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 / 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
Transferrin-binding protein B, N-lobe handle / 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 / Serotransferrin, mammalian / Transferrin-like domain signature 2. ...Transferrin-binding protein B, N-lobe handle / 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 / Serotransferrin, mammalian / 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
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria) / Homo sapiens (human)
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) United States
CitationJournal: To Be Published
Title: NmTbpB and Tf protein complex
Authors: Dubey S / Noinaj N
History
DepositionJun 25, 2025-
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_71436.png

Downloads & links

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Map

FileDownload / File: emd_71436.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 350 pix.
= 374.15 Å		1.07 Å/pix.
x 350 pix.
= 374.15 Å		1.07 Å/pix.
x 350 pix.
= 374.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.069 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.464
Minimum - Maximum-1.0556264 - 2.3273296
Average (Standard dev.)0.004129017 (±0.05581077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 374.15 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71436_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71436_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 : Transferrin Binding protein B in complex with transferrin

EntireName: Transferrin Binding protein B in complex with transferrin
Components
  • Complex: Transferrin Binding protein B in complex with transferrin
    • 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: Transferrin Binding protein B in complex with transferrin

SupramoleculeName: Transferrin Binding protein B in complex with transferrin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Molecular weightTheoretical: 80 KDa

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Supramolecule #2: Tf

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

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Supramolecule #3: TbpB

SupramoleculeName: TbpB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)

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Macromolecule #1: Transferrin

MacromoleculeName: Transferrin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.153906 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 CTFRRP

UniProtKB: Serotransferrin

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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: 77.939453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHDYDI PTTENLYFQG AMLGGGGSFD LDSVDTEAPR PAPKYQDVFS EKPQAQKDQG GYGFAMRLKR RNWYPQAKED EVKLDESDW EATGLPDEPK ELPKRQKSVI EKVETDSDNN IYSSPYLKPS NHQNGNTGNG INQPKNQAKD YENFKYVYSG W FYKHAKRE ...String:
HHHHHHDYDI PTTENLYFQG AMLGGGGSFD LDSVDTEAPR PAPKYQDVFS EKPQAQKDQG GYGFAMRLKR RNWYPQAKED EVKLDESDW EATGLPDEPK ELPKRQKSVI EKVETDSDNN IYSSPYLKPS NHQNGNTGNG INQPKNQAKD YENFKYVYSG W FYKHAKRE FNLKVEPKSA KNGDDGYIFY HGKEPSRQLP ASGKITYKGV WHFATDTKKG QKFREIIQPS KSQGDRYSGF SG DDGEEYS NKNKSTLTDG QEGYGFTSNL EVDFHNKKLT GKLIRNNANT DNNQATTTQY YSLEAQVTGN RFNGKATATD KPQ QNSETK EHPFVSDSSS LSGGFFGPQG EELGFRFLSD DQKVAVVGSA KTKDKPANGN TAAASGGTDA AASNGAAGTS SENG KLTTV LDAVELKLGD KKVQKLDNFS NAAQLVVDGI MIPLLPEASE SGNNQANQGT NGGTAFTRKF DHTPESDKKD AQAGT QTNG AQTASNTAGD TNGKTKTYEV EVCCSNLNYL KYGMLTRKNS KSAMQAGESS SQADAKTEQV EQSMFLQGER TDEKEI PSE QNIVYRGSWY GYIANDKSTS WSGNASNATS GNRAEFTVNF ADKKITGTLT ADNRQEATFT IDGNIKDNGF EGTAKTA ES GFDLDQSNTT RTPKAYITDA KVQGGFYGPK AEELGGWFAY PGDKQTKNAT NASGNSSATV VFGAKRQQPV Q

UniProtKB: Transferrin-binding protein B

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Macromolecule #3: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 3 / 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 #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.3 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 85624
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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