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- EMDB-70277: The structure of TdfH from Neisseria gonorrhoeae -

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Basic information

Entry
Database: EMDB / ID: EMD-70277
TitleThe structure of TdfH from Neisseria gonorrhoeae
Map data
Sample
  • Complex: TdfH and calprotectin complex
    • Protein or peptide: TonB-dependent receptor
    • Protein or peptide: Protein S100-A8
    • Protein or peptide: Protein S100-A9
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
Keywordsouter membrane protein / metal transport / gram-negative bacteria / Neisseria / tonB dependent transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


S100A8 complex / S100A9 complex / neutrophil aggregation / calprotectin complex / regulation of respiratory burst involved in inflammatory response / positive regulation of peptide secretion / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Toll-like receptor 4 binding ...S100A8 complex / S100A9 complex / neutrophil aggregation / calprotectin complex / regulation of respiratory burst involved in inflammatory response / positive regulation of peptide secretion / autocrine signaling / chronic inflammatory response / peptidyl-cysteine S-trans-nitrosylation / Toll-like receptor 4 binding / siderophore transmembrane transport / peptidyl-cysteine S-nitrosylation / Metal sequestration by antimicrobial proteins / siderophore uptake transmembrane transporter activity / peptide secretion / RAGE receptor binding / leukocyte migration involved in inflammatory response / Regulation of TLR by endogenous ligand / astrocyte development / intermediate filament cytoskeleton / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / arachidonate binding / response to zinc ion / regulation of toll-like receptor signaling pathway / regulation of cytoskeleton organization / antioxidant activity / RHO GTPases Activate NADPH Oxidases / defense response to fungus / endothelial cell migration / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / cell outer membrane / positive regulation of neuron projection development / : / autophagy / positive regulation of inflammatory response / calcium-dependent protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / : / ER-Phagosome pathway / positive regulation of cell growth / response to ethanol / secretory granule lumen / response to lipopolysaccharide / microtubule binding / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / 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 / 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 ...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 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsBera A / Noinaj N
Funding support United States, 2 items
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: 2025
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70277.png

Downloads & links

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Map

FileDownload / File: emd_70277.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 269.824 Å		1.05 Å/pix.
x 256 pix.
= 269.824 Å		1.05 Å/pix.
x 256 pix.
= 269.824 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1409042 - 1.4057132
Average (Standard dev.)0.0022233382 (±0.03721932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 269.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70277_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70277_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : TdfH and calprotectin complex

EntireName: TdfH and calprotectin complex
Components
  • Complex: TdfH and calprotectin complex
    • Protein or peptide: TonB-dependent receptor
    • Protein or peptide: Protein S100-A8
    • Protein or peptide: Protein S100-A9
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: TdfH and calprotectin complex

SupramoleculeName: TdfH and calprotectin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Neisseria gonorrhoeae FA 1090 (bacteria)

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Macromolecule #1: TonB-dependent receptor

MacromoleculeName: TonB-dependent receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria gonorrhoeae FA 1090 (bacteria)
Molecular weightTheoretical: 101.58093 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GAMGEDAGRA GSEAQIQVLE DVHVKAKRVP KDKKVFTDAR AVSTRQDVFK SGENLDNIVR SIPGAFTQQD KSSGIVSLNI RGDSGFGRV NTMVDGITQT FYSTSTDAGR AGGSSQFGAS VDSNFIAGLD VVKGSFSGSA GINSLAGSAN LRTLGVDDVV Q GNNTYGLL ...String:
GAMGEDAGRA GSEAQIQVLE DVHVKAKRVP KDKKVFTDAR AVSTRQDVFK SGENLDNIVR SIPGAFTQQD KSSGIVSLNI RGDSGFGRV NTMVDGITQT FYSTSTDAGR AGGSSQFGAS VDSNFIAGLD VVKGSFSGSA GINSLAGSAN LRTLGVDDVV Q GNNTYGLL LKGLTGTNST KGNAMAAIGA RKWLESGASV GVLYGHSRRG VAQNYRVGGG GQHIGNFGEE YLERRKQQYF VQ EGGLKFN AGSGKWERDL QRQYWKTKWY KKYEDPQELQ KYIEEHDKSW RENLAPQYDI TPIDPSGLKQ QSAGNLFKLE YDG VFNKYT AQFRDLNTRI GSRKIINRNY QFNYGLSLNP YTNLNLTAAY NSGRQKYPKG AKFTGWGLLK DFETYNNAKI LDLN NTATF RLPRETELQT TLGFNYFHNE YGKNRFPEEL GLFFDGPDQD NGLYSYLGRF KGDKGLLPQK STIVQPAGSQ YFNTF YFDA ALKKDIYRLN YSTNAINYRF GGEYTGYYGS ENEFKRAFGE NSPAYKEHCD PSCGLYEPVL KKYGKKRANN HSVSIS ADF GDYFMPFAGY SRTHRMPNIQ EMYFSQIGDS GVHTALKPER ANTWQFGFNT YKKGLLKQDD ILGLKLVGYR SRIDNYI HN VYGKWWDLNG DIPSWVGSTG LAYTIRHRNF KDKVHKHGFE LELNYDYGRF FTNLSYAYQK STQPTNFSDA SESPNNAS K EDQLKQGYGL SRVSALPRDY GRLEVGTRWL GNKLTLGGAM RYFGKSIRAT AEERYIDGTN GGNTSNVRQL GKRSIKQTE TLARQPLIFD FYAAYEPKKN LIFRAEVKNL FDRRYIDPLD AGNDAATQRY YSSFDPKDKD EDVTCNADKT LCNGKYGGTS KSVLTNFAR GRTFLMTMSY KF

UniProtKB: TonB-dependent receptor

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Macromolecule #2: Protein S100-A8

MacromoleculeName: Protein S100-A8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.789375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MLTELEKALN SIIDVYHKYS LIKGNFHAVY RDDLKKLLET ESPQYIRKKG ADVWFKELDI NTDGAVNFQE FLILVIKMGV AANKKSNEE SHKE

UniProtKB: Protein S100-A8

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Macromolecule #3: Protein S100-A9

MacromoleculeName: Protein S100-A9 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.211966 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTCKMSQLER NIETIINTFN QYSVKLGHPS TLNQGEFKEL VRKDLQNFLK KENKNEKVIE HIMEDLDTNA DKQLSFEEFI MLMARLTWA SHEKMHEGDE GPGHHHKPGL GEGTP

UniProtKB: Protein S100-A9

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.4 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 70585
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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