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- EMDB-43346: TolQ-TolR inner membrane protein complex from Acinetobacter baumannii -

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Basic information

Entry
Database: EMDB / ID: EMD-43346
TitleTolQ-TolR inner membrane protein complex from Acinetobacter baumannii
Map dataTolQ-TolR inner membrane protein complex from Acinetobacter baumannii
Sample
  • Complex: TolQ-TolR inner membrane protein complex
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolR
Keywordsinner membrane protein complex / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / MEMBRANE PROTEIN
Function / homology
Function and homology information


bacteriocin transport / protein import / transmembrane transporter activity / protein transport / cell division / plasma membrane
Similarity search - Function
Tol-Pal system, TolQ / Tol-Pal system protein TolR / : / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Tol-Pal system protein TolR / Tol-Pal system protein TolQ
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsGuo Y / Borek D / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2024
Title: Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen .
Authors: Elina Karimullina / Yirui Guo / Hanif M Khan / Tabitha Emde / Bradley Quade / Rosa Di Leo / Zbyszek Otwinowski / D Tieleman Peter / Dominika Borek / Alexei Savchenko
Abstract: Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. ...Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo-EM reconstructions of TolQ in apo and TolR- bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a trans-membrane funnel leading towards a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton non-permeable stance, characterized by the TolQ pentamer's flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers' interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.
TEASER: Apo TolQ and TolQ-TolR structures depict structural rearrangements required for cell envelope organization in bacterial cell division.
History
DepositionJan 12, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43346.png

Downloads & links

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Map

FileDownload / File: emd_43346.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTolQ-TolR inner membrane protein complex from Acinetobacter baumannii
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 360.288 Å		0.83 Å/pix.
x 432 pix.
= 360.288 Å		0.83 Å/pix.
x 432 pix.
= 360.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21220653 - 0.42175624
Average (Standard dev.)0.000057326666 (±0.008469379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 360.288 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_43346_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_43346_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TolQ-TolR inner membrane protein complex

EntireName: TolQ-TolR inner membrane protein complex
Components
  • Complex: TolQ-TolR inner membrane protein complex
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolR

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Supramolecule #1: TolQ-TolR inner membrane protein complex

SupramoleculeName: TolQ-TolR inner membrane protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: Tol-Pal system protein TolQ

MacromoleculeName: Tol-Pal system protein TolQ / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 24.112875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: STLHISDLIL QASPVVQLVM LILLLASIFS WYLIAKLHMS YKKARQDDEH FQKMFWSGAE LNTLYNNAQL NSKRSGLEDI FYQGLSEFF KLKKRQAPTS QMIEGTERIL RVGLSRDQGS LEYGLGTLAS IGSVAPYIGL FGTVWGIMNA FIGLAAVDQV T LATVAPGI ...String:
STLHISDLIL QASPVVQLVM LILLLASIFS WYLIAKLHMS YKKARQDDEH FQKMFWSGAE LNTLYNNAQL NSKRSGLEDI FYQGLSEFF KLKKRQAPTS QMIEGTERIL RVGLSRDQGS LEYGLGTLAS IGSVAPYIGL FGTVWGIMNA FIGLAAVDQV T LATVAPGI AEALIATAIG LFAAIPAVLA FNHFTAKSES VYSDRALFAE EMIALLQRQS VG

UniProtKB: Tol-Pal system protein TolQ

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Macromolecule #2: Tol-Pal system protein TolR

MacromoleculeName: Tol-Pal system protein TolR / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 4.471523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GRFERIKKPL KSDMNVVPYI DVMLVLLVIF MVTAPMITS

UniProtKB: Tol-Pal system protein TolR

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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: PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224768
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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