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- EMDB-43902: TolQ inner membrane protein from Acinetobacter baumannii -

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Basic information

Entry
Database: EMDB / ID: EMD-43902
TitleTolQ inner membrane protein from Acinetobacter baumannii
Map dataTolQ inner membrane protein from Acinetobacter baumannii
Sample
  • Organelle or cellular component: TolQ inner membrane protein
    • Protein or peptide: Tol-Pal system protein TolQ
Keywordsinner membrane protein complex / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / MEMBRANE PROTEIN
Function / homologyTol-Pal system, TolQ / : / bacteriocin transport / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / protein import / cell division / plasma membrane / Tol-Pal system protein TolQ
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsQuade B / Otwinowski Z / Borek D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 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
DepositionMar 3, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43902.png

Downloads & links

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Map

FileDownload / File: emd_43902.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTolQ inner membrane protein from Acinetobacter baumannii
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 333.2 Å		0.83 Å/pix.
x 400 pix.
= 333.2 Å		0.83 Å/pix.
x 400 pix.
= 333.2 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.19440597 - 0.4497866
Average (Standard dev.)0.00025368002 (±0.009321547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_43902_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_43902_half_map_2.map
AnnotationHalf Map B
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : TolQ inner membrane protein

EntireName: TolQ inner membrane protein
Components
  • Organelle or cellular component: TolQ inner membrane protein
    • Protein or peptide: Tol-Pal system protein TolQ

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Supramolecule #1: TolQ inner membrane protein

SupramoleculeName: TolQ inner membrane protein / type: organelle_or_cellular_component / 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: 25.390193 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATNIESTLH ISDLILQASP VVQLVMLILL LASIFSWYLI AKLHMSYKKA RQDDEHFQKM FWSGAELNTL YNNAQLNSKR SGLEDIFYQ GLSEFFKLKK RQAPTSQMIE GTERILRVGL SRDQGSLEYG LGTLASIGSV APYIGLFGTV WGIMNAFIGL A AVDQVTLA ...String:
MATNIESTLH ISDLILQASP VVQLVMLILL LASIFSWYLI AKLHMSYKKA RQDDEHFQKM FWSGAELNTL YNNAQLNSKR SGLEDIFYQ GLSEFFKLKK RQAPTSQMIE GTERILRVGL SRDQGSLEYG LGTLASIGSV APYIGLFGTV WGIMNAFIGL A AVDQVTLA TVAPGIAEAL IATAIGLFAA IPAVLAFNHF TAKSESVYSD RALFAEEMIA LLQRQSVGSS QEDA

UniProtKB: Tol-Pal system protein TolQ

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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

Concentration5.7 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Name: TRIS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details50mM Tris pH 8.0; 150mM NaCl; 0.5 mM TCEP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2718 / Average exposure time: 4.4 sec. / Average electron dose: 100.0 e/Å2
Details: Images were collected as movies, with each movie containing 125 frames. The beam-image shift method, utilizing a 3x3 pattern, was used, with one image per grid hole.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsPatch motion and patch CTF correction with binning to 0.833 A/pixel.
Particle selectionNumber selected: 472724
Details: Manual picking to generate templates. Template based autopicking to get 472724 particles. Iterative 2D classification to get 246741 particles.
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Map was post processed using DeepEMHancer to guide refinement. The deposited maps are pre-DeepEMHancer
Number images used: 215170
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
Output model

PDB-9avi:
TolQ inner membrane protein from Acinetobacter baumannii

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