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- EMDB-63539: Structure of outer membrane lipoprotein QseG and histidine kinase... -

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Basic information

Entry
Database: EMDB / ID: EMD-63539
TitleStructure of outer membrane lipoprotein QseG and histidine kinase QseE complex
Map data
Sample
  • Complex: QseG58-220 and QseE sensor complex
    • Protein or peptide: Quorum-sensing regulator protein G
    • Protein or peptide: histidine kinase
Keywordscomplex / SIGNALING PROTEIN
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / ATP binding / plasma membrane
Similarity search - Function
Quorum-sensing regulator protein G / YfhG lipoprotein / : / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain ...Quorum-sensing regulator protein G / YfhG lipoprotein / : / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Hypothetical membrane protein / histidine kinase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGao X / Li GB / Gong PQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200144 China
CitationJournal: mBio / Year: 2025
Title: Cryo-EM structure of the QseG-QseE complex reveals an accessory protein-driven two-component system activation mechanism.
Authors: Piqian Gong / Guobang Li / Weixun Li / Mengyuan Xu / Xuyao Jiao / Xudong Chen / Beile Gao / Xiang Gao /
Abstract: The two-component system (TCS) enables bacteria to sense and respond to environmental changes through histidine kinase-mediated signaling cascades. Although the core components of TCSs have been ...The two-component system (TCS) enables bacteria to sense and respond to environmental changes through histidine kinase-mediated signaling cascades. Although the core components of TCSs have been extensively studied, the molecular basis of accessory proteins in modulating histidine kinase activity remains poorly understood. Here, we report that the outer membrane lipoprotein QseG functions as an accessory protein that directly binds to and activates the histidine kinase QseE via its C-terminal domain. Cryo-electron microscopy (Cryo-EM) structural analysis of the QseG-QseE complex reveals a novel yet conserved interaction mode between an accessory lipoprotein and a histidine kinase, which bridges the outer membrane to cytoplasm. Furthermore, systematic truncation assays and photo-crosslinking experiments indicate that outer membrane-anchored QseG is sufficient and prone to engage with and activate the inner membrane histidine kinase QseE under cultured conditions. Our findings provide mechanistic details for accessory lipoprotein-mediated TCS activation, expanding our understanding of bacterial signaling. The evolutionary conservation of this interaction across bacterial pathogens underscores its broad biological significance and potential as a therapeutic target.IMPORTANCEThe classical TCS system in bacterial signal transduction is composed of two proteins-a histidine kinase and its cognate response regulator. More and more studies have revealed the presence of accessory proteins that can modulate the histidine kinase activity and affect signal transduction, but their mechanisms remain largely elusive. This study unveils a previously unrecognized mechanism by which bacterial accessory lipoproteins mediate TCS activation. We provide compelling evidence that QseG directly interacts with QseE through an evolutionarily conserved structural interface, readily and sufficiently activating QseE's autokinase activity and downstream signaling. Given the essential role of QseEF in bacterial virulence and stress adaptation, our findings pave the way for the development of antimicrobial strategies targeting this conserved lipoprotein-mediated activation mechanism.
History
DepositionFeb 24, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63539.png

Downloads & links

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Map

FileDownload / File: emd_63539.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6186836 - 0.84543645
Average (Standard dev.)0.000066890534 (±0.009750224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63539_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_63539_half_map_2.map
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Sample components

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Entire : QseG58-220 and QseE sensor complex

EntireName: QseG58-220 and QseE sensor complex
Components
  • Complex: QseG58-220 and QseE sensor complex
    • Protein or peptide: Quorum-sensing regulator protein G
    • Protein or peptide: histidine kinase

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Supramolecule #1: QseG58-220 and QseE sensor complex

SupramoleculeName: QseG58-220 and QseE sensor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)

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Macromolecule #1: Quorum-sensing regulator protein G

MacromoleculeName: Quorum-sensing regulator protein G / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Molecular weightTheoretical: 21.02274 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
CVPHASQQLP GSAAQDTLPH YQLADYLPTA CADIWSLRGQ AVETNPLYWL RTIDCADRLM PVQSRAEARA LTDDNWQNAF RRGILLADA KITPPERRAI VTRLEALSAQ IPAQVRPVYQ IWHDGQALQL ALSAERQRYS KLQQMSDSEL DALRQQQQAL Q TQLDLTTR KLESLTDIER QLSTRKP

UniProtKB: Hypothetical membrane protein

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Macromolecule #2: histidine kinase

MacromoleculeName: histidine kinase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Molecular weightTheoretical: 54.747652 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKRWSVFPRS LRQLVMLAFL LILLPLLVLA WQAWQSLNAL SDQAAVTNRS TLIDARRSEA MTNVALEMER SYRQYCVLDD PTLAKVYQS QRKRYSDMLD AHAGVLPDDK LYQALRQDLN ALAQLQCKDS GPEAAAAARL EAFANANTEM VQATRTVVYS R GQQLQQEI ...String:
MKRWSVFPRS LRQLVMLAFL LILLPLLVLA WQAWQSLNAL SDQAAVTNRS TLIDARRSEA MTNVALEMER SYRQYCVLDD PTLAKVYQS QRKRYSDMLD AHAGVLPDDK LYQALRQDLN ALAQLQCKDS GPEAAAAARL EAFANANTEM VQATRTVVYS R GQQLQQEI AERGQFFGWQ ALVLFLVSLA MVLLFTRMII GPVKGIERMI NRLGEGRSLG NTVTFTGPRE LRSVGQRIIW LS ERLAWLE SQRHQFLRHL SHELKTPLAS MREGTELLAD QVVGPLTPEQ KEVVDILDDS SRNLQKLIEQ LLDYNRKLVD SAT ELEAVD IAPLVDMVVS AHSLPARAKM MHTDVDLEAE RCIAEPMLLM SVLDNLYSNA VHYGAESGNI CIRSRSQGST VYID VVNSG EPIPQTEREM IFEPFFQGSH QRKGAVKGSG LGLSIARDCI RRMQGEIQLV DDNAQEVCFR ISLPLPASDK HGSWS HPQF EK

UniProtKB: histidine kinase

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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: 8
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88834
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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