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- PDB-9yz4: Neisseria gonorrhoeae Transferrin Binding Protein A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9yz4
TitleNeisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only)
Components
  • Transferrin
  • Transferrin-binding protein A
  • Transferrin-binding protein B
KeywordsTRANSPORT PROTEIN / Membrane protein / metal transporter / iron import / ton B-dependent transporter
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 / 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
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
BICARBONATE ION / : / Serotransferrin / Transferrin-binding protein A / Transferrin-binding protein B
Similarity search - Component
Biological speciesHomo sapiens (human)
Neisseria gonorrhoeae (bacteria)
Neisseria meningitidis serogroup B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.26 Å
AuthorsDubey, S. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
CitationJournal: To Be Published
Title: Neisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only)
Authors: Dubey, S. / Noinaj, N.
History
DepositionOct 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Transferrin
A: Transferrin-binding protein A
B: Transferrin-binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,7925
Polymers254,6753
Non-polymers1172
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Transferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 77153.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / Production host: Homo sapiens (human) / References: UniProt: P02787
#2: Protein Transferrin-binding protein A / TbpA / Transferrin-binding protein 1


Mass: 102036.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: tbpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q01996
#3: Protein Transferrin-binding protein B


Mass: 75484.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: tbpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JPI9
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Transferrin binding protein A/ B/TfCOMPLEX#3, #1-#20RECOMBINANT
2NgTbpACOMPLEX#21RECOMBINANT
3TfCOMPLEX#11NATURAL
4NmTbpBCOMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.1 MDaNO
210.1 MDaNO
310.08 MDaNO
410.088 MDaNO
64
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Neisseria meningitidis serogroup B (bacteria)491
32Neisseria gonorrhoeae (bacteria)485
43Homo sapiens (human)9606
54Neisseria meningitidis serogroup B (bacteria)491
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
32Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
43Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
54Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 7.8
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 53.52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20_4459model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2588171
3D reconstructionResolution: 4.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 4.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217697
ELECTRON MICROSCOPYf_angle_d0.61223910
ELECTRON MICROSCOPYf_dihedral_angle_d5.0392447
ELECTRON MICROSCOPYf_chiral_restr0.0422499
ELECTRON MICROSCOPYf_plane_restr0.0043177

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