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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: Gao X / Li GB / Gong PQ
History
DepositionFeb 24, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 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
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63539_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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