[English] 日本語
Yorodumi
- PDB-9oaa: The structure of TdfH from Neisseria gonorrhoeae -

+
Open data


ID or keywords:

Loading...

-
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


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)
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: 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, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more