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- PDB-9oaa: The structure of TdfH from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 9oaa
TitleThe structure of TdfH from Neisseria gonorrhoeae
Components
  • Protein S100-A8
  • Protein S100-A9
  • TonB-dependent receptor
KeywordsMEMBRANE PROTEIN / outer membrane protein / metal transport / gram-negative bacteria / Neisseria / tonB dependent transporter
Function / homology
Function and homology information


neutrophil aggregation / regulation of respiratory burst involved in inflammatory response / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Toll-like receptor 4 binding / regulation of toll-like receptor signaling pathway / siderophore transmembrane transport / autocrine signaling / Metal sequestration by antimicrobial proteins / Scavenging by Class B Receptors ...neutrophil aggregation / regulation of respiratory burst involved in inflammatory response / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Toll-like receptor 4 binding / regulation of toll-like receptor signaling pathway / siderophore transmembrane transport / autocrine signaling / Metal sequestration by antimicrobial proteins / Scavenging by Class B Receptors / astrocyte development / siderophore uptake transmembrane transporter activity / leukocyte migration involved in inflammatory response / intermediate filament cytoskeleton / RAGE receptor binding / Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / arachidonate binding / IRAK4 deficiency (TLR2/4) / response to zinc ion / peptidyl-cysteine S-nitrosylation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / antioxidant activity / regulation of cytoskeleton organization / defense response to fungus / RHO GTPases Activate NADPH Oxidases / endothelial cell migration / neutrophil chemotaxis / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of neuron projection development / cell outer membrane / autophagy / positive regulation of inflammatory response / calcium-dependent protein binding / cell-cell signaling / positive regulation of cell growth / response to lipopolysaccharide / ER-Phagosome pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / secretory granule lumen / extracellular matrix / microtubule binding / response to ethanol / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / : / extracellular exosome / extracellular region / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / 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, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / TonB-dependent Receptor Plug Domain / S-100/ICaBP type calcium binding domain / TonB-dependent receptor-like, beta-barrel domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Protein S100-A8 / Protein S100-A9 / TonB-dependent receptor
Similarity search - Component
Biological speciesNeisseria gonorrhoeae FA 1090 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsBera, A. / Noinaj, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI127793 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI144182 United States
CitationJournal: Structure / Year: 2026
Title: Structural insights into zinc piracy by Neisseria gonorrhoeae to overcome nutritional immunity.
Authors: Pooneh Tavakoley Gheinani / Aloke Bera / Julie Stoudenmire-Saylor / Yi Lien / Simone A Harrison / Alison Criss / Walter J Chazin / Nicholas Noinaj / Cynthia Nau Cornelissen /
Abstract: With an estimated 106 million global cases annually, Neisseria gonorrhoeae (Ngo) poses a significant public health problem. Ngo demonstrates a remarkable capacity to overcome nutritional immunity ...With an estimated 106 million global cases annually, Neisseria gonorrhoeae (Ngo) poses a significant public health problem. Ngo demonstrates a remarkable capacity to overcome nutritional immunity through the deployment of specialized transporters that pirate metals such as zinc from human proteins such as calprotectin (hCP). We report the cryo-EM structure of Ngo TdfH in complex with a heterotetramer of hCP. An extensive binding interface is mediated almost entirely by the S100A9 subunits of hCP. Mutagenesis studies of residues in the large binding interface reveal minimal effects from single-site mutations, whereas larger truncations disrupt binding and function. These results support a mechanistic model based on the large interaction interface overcoming a steric clash between α-helix III of S100A9 and loops 5 and 9 of TdfH, which leads to the distortion of the proximal His6 site, followed by zinc release, and import through the barrel domain.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: TonB-dependent receptor
A: Protein S100-A8
B: Protein S100-A9
C: Protein S100-A8
D: Protein S100-A9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,84911
Polymers149,5845
Non-polymers2666
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 TonB-dependent receptor


Mass: 101580.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA 1090 (bacteria)
Gene: NGO_0952 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F845
#2: Protein Protein S100-A8 / Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex ...Calgranulin-A / Calprotectin L1L subunit / Cystic fibrosis antigen / CFAG / Leukocyte L1 complex light chain / Migration inhibitory factor-related protein 8 / MRP-8 / p8 / S100 calcium-binding protein A8 / Urinary stone protein band A


Mass: 10789.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A8, CAGA, CFAG, MRP8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05109
#3: Protein Protein S100-A9 / Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory ...Calgranulin-B / Calprotectin L1H subunit / Leukocyte L1 complex heavy chain / Migration inhibitory factor-related protein 14 / MRP-14 / p14 / S100 calcium-binding protein A9


Mass: 13211.966 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A9, CAGB, CFAG, MRP14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06702
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / 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

ComponentName: TdfH and calprotectin complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Neisseria gonorrhoeae FA 1090 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: 1500 nm
Image recordingElectron dose: 45.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70585 / Symmetry type: POINT

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