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- EMDB-70142: E. coli TolAQR -

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Basic information

Entry
Database: EMDB / ID: EMD-70142
TitleE. coli TolAQR
Map dataE. coli TolAQR complex in DMNG
Sample
  • Complex: TolAQR complex
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolA
    • Protein or peptide: Tol-Pal system protein TolR
KeywordsTol-Pal system / TolAQR / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsCelia H / Botos I
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK011011-17 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the E. coli Ton and Tol motor complexes
Authors: Celia H / Botos I / Ghirlando R / Duche D / Beach BM / Lloubes R / Buchanan SK
History
DepositionApr 10, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70142.png

Downloads & links

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Map

FileDownload / File: emd_70142.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli TolAQR complex in DMNG
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 128 pix.
= 227.84 Å		1.78 Å/pix.
x 128 pix.
= 227.84 Å		1.78 Å/pix.
x 128 pix.
= 227.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.19457503 - 0.6236872
Average (Standard dev.)0.004395328 (±0.034589283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 227.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_70142_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap A

Fileemd_70142_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_70142_half_map_2.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TolAQR complex

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

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Supramolecule #1: TolAQR complex

SupramoleculeName: TolAQR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Tol-Pal system protein TolQ

MacromoleculeName: Tol-Pal system protein TolQ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDMNILDLF LKASLLVKLI MLILIGFSIA SWAIIIQRTR ILNAAAREAE AFEDKFWSGI ELSRLYQESQ GKRDNLTGSE QIFYSGFKE FVRLHRANSH APEAVVEGAS RAMRISMNRE LENLETHIPF LGTVGSISPY IGLFGTVWGI MHAFIALGAV K QATLQMVA ...String:
MTDMNILDLF LKASLLVKLI MLILIGFSIA SWAIIIQRTR ILNAAAREAE AFEDKFWSGI ELSRLYQESQ GKRDNLTGSE QIFYSGFKE FVRLHRANSH APEAVVEGAS RAMRISMNRE LENLETHIPF LGTVGSISPY IGLFGTVWGI MHAFIALGAV K QATLQMVA PGIAEALIAT AIGLFAAIPA VMAYNRLNQR VNKLELNYDN FMEEFTAILH RQAFTVSESN KG

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Macromolecule #2: Tol-Pal system protein TolA

MacromoleculeName: Tol-Pal system protein TolA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSWSHPQFE KGSSKATEQN DKLKRAIIIS AVLHVILFAA LIWSSFDENI EASAGGGGGS SIDAVMVDSG AVVEQYKRMQ SQESSAKRS DEQRKMKEQQ AAEELREKQA AEQERLKQLE KERLAAQEQK KQAEEAAKQA ELKQKQAEEA AAKAAADAKA K AEADAKAA ...String:
MGSWSHPQFE KGSSKATEQN DKLKRAIIIS AVLHVILFAA LIWSSFDENI EASAGGGGGS SIDAVMVDSG AVVEQYKRMQ SQESSAKRS DEQRKMKEQQ AAEELREKQA AEQERLKQLE KERLAAQEQK KQAEEAAKQA ELKQKQAEEA AAKAAADAKA K AEADAKAA EEAAKKAAAD AKKKAEAEAA KAAAEAQKKA EAAAAALKKK AEAAEAAAAE ARKKAATEAA EKAKAEAEKK AA AEKAAAD KKAAAEKAAA DKKAAEKAAA EKAAADKKAA AEKAAADKKA AAAKAAAEKA AAAKAAAEAD DIFGELSSGK NAP KTGGGA KGNNASPAGS GNTKNNGASG ADINNYAGQI KSAIESKFYD ASSYAGKTCT LRIKLAPDGM LLDIKPEGGD PALC QAALA AAKLAKIPKP PSQAVYEVFK NAPLDFKP

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Macromolecule #3: Tol-Pal system protein TolR

MacromoleculeName: Tol-Pal system protein TolR / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARARGRGRR DLKSEINIVP LLDVLLVLLL IFMATAPIIT QSVEVDLPDA TESQAVSSND NPPVIVEVSG IGQYTVVVEK DRLERLPPE QVVAEVSSRF KANPKTVFLI GGAKDVPYDE IIKALNLLHS AGVKSVGLMT QPI

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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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: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107631
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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