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- PDB-9nhq: The cryo-EM structure of NmTbpA and NmTbpB in a complex -

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Basic information

Entry
Database: PDB / ID: 9nhq
TitleThe cryo-EM structure of NmTbpA and NmTbpB in a complex
Components
  • Transferrin-binding protein A
  • Transferrin-binding protein B
KeywordsMEMBRANE PROTEIN / Neisseria outer membrane protein / Ton B dependent transporter / lipo protein / iron transport
Function / homology
Function and homology information


ferric iron transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane / cell surface
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. / 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 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Transferrin-binding protein B / Transferrin-binding protein A
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDubey, S.D. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
CitationJournal: To Be Published
Title: The cryo-EM structure of NmTbpA and NmTbpB in a complex
Authors: Dubey, S.D. / Noinaj, N.
History
DepositionFeb 25, 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

Downloads & links

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Assembly

Deposited unit
A: Transferrin-binding protein A
B: Transferrin-binding protein B


Theoretical massNumber of molelcules
Total (without water)180,4462
Polymers180,4462
Non-polymers00
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-binding protein A / Transferrin-binding protein 1


Mass: 102506.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: tbpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JPJ0
#2: Protein Transferrin-binding protein B


Mass: 77939.453 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
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
1NmTbpA/NmTbpBCOMPLEXall0RECOMBINANT
2NmTbpACOMPLEX#11RECOMBINANT
3NmTbpBCOMPLEX1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.180 MDaNO
210.1 MDaNO
310.08 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Neisseria meningitidis (bacteria)487
32Neisseria meningitidis (bacteria)487
43Neisseria meningitidis (bacteria)487
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
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: 1200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18rc1_3777: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38789 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210974
ELECTRON MICROSCOPYf_angle_d0.53614858
ELECTRON MICROSCOPYf_dihedral_angle_d4.1531539
ELECTRON MICROSCOPYf_chiral_restr0.0411560
ELECTRON MICROSCOPYf_plane_restr0.0031970

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