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- EMDB-45682: Transferrin Binding Protein A in complex with transferrin binding... -

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Basic information

Entry
Database: EMDB / ID: EMD-45682
TitleTransferrin Binding Protein A in complex with transferrin binding protein B and two molecules of transferrin
Map data
Sample
  • Complex: TbpA/TbpB/Tf(2x)
    • Complex: TbpA
      • Protein or peptide: Transferrin Binding Protein A
    • Complex: TbpB
      • Protein or peptide: Transferrin Binding Protein B
    • Organelle or cellular component: Tf
      • Protein or peptide: Transferrin
  • 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 / 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
Transferrin-binding protein A / Serotransferrin / Transferrin-binding protein B
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDubey S / Noinaj N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR002529 United States
CitationJournal: To Be Published
Title: Transferrin Binding Protein A in complex with transferrin binding protein B and two molecules of transferrin
Authors: Dubey S / Noinaj N
History
DepositionJul 11, 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_45682.png

Downloads & links

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Map

FileDownload / File: emd_45682.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 323.4 Å		1.08 Å/pix.
x 300 pix.
= 323.4 Å		1.08 Å/pix.
x 300 pix.
= 323.4 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: 0.0888
Minimum - Maximum-0.16007839 - 0.43539938
Average (Standard dev.)0.002576886 (±0.01778068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 323.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45682_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_45682_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 : TbpA/TbpB/Tf(2x)

EntireName: TbpA/TbpB/Tf(2x)
Components
  • Complex: TbpA/TbpB/Tf(2x)
    • Complex: TbpA
      • Protein or peptide: Transferrin Binding Protein A
    • Complex: TbpB
      • Protein or peptide: Transferrin Binding Protein B
    • Organelle or cellular component: Tf
      • Protein or peptide: Transferrin
  • Ligand: BICARBONATE ION
  • Ligand: FE (III) ION

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Supramolecule #1: TbpA/TbpB/Tf(2x)

SupramoleculeName: TbpA/TbpB/Tf(2x) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 80 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: TbpB

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

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Supramolecule #4: Tf

SupramoleculeName: Tf / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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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: 105.3575 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNHHHHHHH HHHENLYFQG AMDIMQQQHL FRLNILCLSL MTALPAYAEN VQAGQAQEKQ LDTIQVKAKK QKTRRDNEVT GLGKLVKTA DTLSKEQVLD IRDLTRYDPG IAVVEQGRGA SSGYSIRGMD KNRVSLTVDG LAQIQSYTAQ AALGGTRTAG S SGAINEIE ...String:
MSNHHHHHHH HHHENLYFQG AMDIMQQQHL FRLNILCLSL MTALPAYAEN VQAGQAQEKQ LDTIQVKAKK QKTRRDNEVT GLGKLVKTA DTLSKEQVLD IRDLTRYDPG IAVVEQGRGA SSGYSIRGMD KNRVSLTVDG LAQIQSYTAQ AALGGTRTAG S SGAINEIE YENVKAVEIS KGSNSVEQGS GALAGSVAFQ TKTADDVIGE GRQWGIQSKT AYSGKNRGLT QSIALAGRIG GA EALLIRT GRHAGEIRAH EAAGRGVQSF NRLAPVDDGS KYAYFIVEEE CKNGGHEKCK ANPKKDVVGE DKRQTVSTRD YTG PNRFLA DPLSYESRSW LFRPGFRFEN KRHYIGGILE RTQQTFDTRD MTVPAFLTKA VFDANQKQAG SLRGNGKYAG NHKY GGLFT SGENNAPVGA EYGTGVFYDE THTKSRYGLE YVYTNADKDT WADYARLSYD RQGIGLDNHF QQTHCSADGS DKYCR PSAD KPFSYYKSDR VIYGESHKLL QAAFKKSFDT AKIRHNLSVN LGYDRFGSNL RHQDYYYQSA NRAYSLKTPP QNNGKK TSP NGREKNPYWV SIGRGNVVTR QICLFGNNTY TDCTPRSING KSYYAAVRDN VRLGRWADVG AGLRYDYRST HSDDGSV ST GTHRTLSWNA GIVLKPADWL DLTYRTSTGF RLPSFAEMYG WRSGDKIKAV KIDPEKSFNK EAGIVFKGDF GNLEASWF N NAYRDLIVRG YEAQIKDGKE QVKGNPAYLN AQSARITGIN ILGKIDWNGV WDKLPEGWYS TFAYNRVRVR DIKKRADRT DIQSHLFDAI QPSRYVVGSG YDQPEGKWGV NGMLTYSKAK EITELLGSRA LLNGNSRNTK ATARRTRPWY IVDVSGYYTV KKHFTLRAG VYNLLNHRYV TWENVRQTAA GAVNQHKNVG VYNRYAAPGR NYTFSLEMKF

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 (bacteria)
Molecular weightTheoretical: 77.478266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNPLVNQAA MVLPVFLLSA CLGGGGSFDL DSVDTEAPRP APKYQDVFSE KPQAQKDQGG YGFAMRLKRR NWYPQAKEDE VKLDESDWE ATGLPDEPKE LPKRQKSVIE KVETDSDNNI YSSPYLKPSN HQNGNTGNGI NQPKNQAKDY ENFKYVYSGW F YKHAKREF ...String:
MNNPLVNQAA MVLPVFLLSA CLGGGGSFDL DSVDTEAPRP APKYQDVFSE KPQAQKDQGG YGFAMRLKRR NWYPQAKEDE VKLDESDWE ATGLPDEPKE LPKRQKSVIE KVETDSDNNI YSSPYLKPSN HQNGNTGNGI NQPKNQAKDY ENFKYVYSGW F YKHAKREF NLKVEPKSAK NGDDGYIFYH GKEPSRQLPA SGKITYKGVW HFATDTKKGQ KFREIIQPSK SQGDRYSGFS GD DGEEYSN KNKSTLTDGQ EGYGFTSNLE VDFHNKKLTG KLIRNNANTD NNQATTTQYY SLEAQVTGNR FNGKATATDK PQQ NSETKE HPFVSDSSSL SGGFFGPQGE ELGFRFLSDD QKVAVVGSAK TKDKPANGNT AAASGGTDAA ASNGAAGTSS ENGK LTTVL DAVELKLGDK KVQKLDNFSN AAQLVVDGIM IPLLPEASES GNNQANQGTN GGTAFTRKFD HTPESDKKDA QAGTQ TNGA QTASNTAGDT NGKTKTYEVE VCCSNLNYLK YGMLTRKNSK SAMQAGESSS QADAKTEQVE QSMFLQGERT DEKEIP SEQ NIVYRGSWYG YIANDKSTSW SGNASNATSG NRAEFTVNFA DKKITGTLTA DNRQEATFTI DGNIKDNGFE GTAKTAE SG FDLDQSNTTR TPKAYITDAK VQGGFYGPKA EELGGWFAYP GDKQTKNATN ASGNSSATVV FGAKRQQPVQ

UniProtKB: Transferrin-binding protein B

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Macromolecule #3: Transferrin

MacromoleculeName: Transferrin / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 4 / Number of copies: 3 / 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: 3 / 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
GridMaterial: COPPER
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 / 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47147
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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