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- EMDB-62492: Structure of TolQRA complex at pH 5.4 from E.coli -

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Basic information

Entry
Database: EMDB / ID: EMD-62492
TitleStructure of TolQRA complex at pH 5.4 from E.coli
Map data
Sample
  • Complex: Tol-Pal system complex TolQRA at pH 5.4 from E. coli
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolR
    • Protein or peptide: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsTolQRA / TolQ / TolR / TolA / Tol-Pal complex / proton transporter / proton motive force / E.coli / Outer membrane / Inner membrane / MEMBRANE PROTEIN
Function / homology
Function and homology information


cellular response to bacteriocin / regulation of membrane invagination / cell septum assembly / bacteriocin transport / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / toxin transmembrane transporter activity / SUMOylation of transcription factors ...cellular response to bacteriocin / regulation of membrane invagination / cell septum assembly / bacteriocin transport / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / toxin transmembrane transporter activity / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / protein import / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / virion binding / SUMOylation of RNA binding proteins / cell envelope / SUMOylation of chromatin organization proteins / cell division site / ubiquitin-like protein ligase binding / protein sumoylation / transmembrane transporter activity / condensed nuclear chromosome / protein tag activity / disordered domain specific binding / protein transport / protein domain specific binding / cell division / symbiont entry into host cell / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
TolA C-terminal / Tol-Pal system, TolQ / Tol-Pal system protein TolR / Tol-Pal system, TolA / : / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / Rad60/SUMO-like domain ...TolA C-terminal / Tol-Pal system, TolQ / Tol-Pal system protein TolR / Tol-Pal system, TolA / : / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tol-Pal system protein TolQ / Tol-Pal system protein TolR / Tol-Pal system protein TolA / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsDong C / Zhang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of TolQRA complex at pH 5.4 from E.coli
Authors: Dong C / Zhang Z
History
DepositionNov 24, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62492.png

Downloads & links

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Map

FileDownload / File: emd_62492.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.7302264 - 1.0993847
Average (Standard dev.)0.000111904454 (±0.023404976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62492_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62492_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62492_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 : Tol-Pal system complex TolQRA at pH 5.4 from E. coli

EntireName: Tol-Pal system complex TolQRA at pH 5.4 from E. coli
Components
  • Complex: Tol-Pal system complex TolQRA at pH 5.4 from E. coli
    • Protein or peptide: Tol-Pal system protein TolQ
    • Protein or peptide: Tol-Pal system protein TolR
    • Protein or peptide: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Tol-Pal system complex TolQRA at pH 5.4 from E. coli

SupramoleculeName: Tol-Pal system complex TolQRA at pH 5.4 from E. coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: MG1655

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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: Escherichia coli K-12 (bacteria) / Strain: MG1655
Molecular weightTheoretical: 25.779844 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGVTDMNILD LFLKASLLVK LIMLILIGFS IASWAIIIQR TRILNAAARE AEAFEDKFWS GIELSRLYQE SQGKRDNLTG SEQIFYSGF KEFVRLHRAN SHAPEAVVEG ASRAMRISMN RELENLETHI PFLGTVGSIS PYIGLFGTVW GIMHAFIALG A VKQATLQM ...String:
MGVTDMNILD LFLKASLLVK LIMLILIGFS IASWAIIIQR TRILNAAARE AEAFEDKFWS GIELSRLYQE SQGKRDNLTG SEQIFYSGF KEFVRLHRAN SHAPEAVVEG ASRAMRISMN RELENLETHI PFLGTVGSIS PYIGLFGTVW GIMHAFIALG A VKQATLQM VAPGIAEALI ATAIGLFAAI PAVMAYNRLN QRVNKLELNY DNFMEEFTAI LHRQAFTVSE SNKG

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: Escherichia coli K-12 (bacteria) / Strain: MG1655
Molecular weightTheoretical: 15.398884 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MARARGRGRR DLKSEINIVP LLDVLLVLLL IFMATAPIIT QSVEVDLPDA TESQAVSSND NPPVIVEVSG IGQYTVVVEK DRLERLPPE QVVAEVSSRF KANPKTVFLI GGAKDVPYDE IIKALNLLHS AGVKSVGLMT QPI

UniProtKB: Tol-Pal system protein TolR

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Macromolecule #3: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA

MacromoleculeName: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: MG1655
Molecular weightTheoretical: 58.492613 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGHHHHHHHH GSLQDSEVNQ EAKPEVKPEV KPETHINLKV SDGSSEIFFK IKKTTPLRRL MEAFAKRQGK EMDSLRFLYD GIRIQADQT PEDLDMEDND IIEAHREQIG GAAADYGGDI PTTENLYFQG AAADIGSVSK ATEQNDKLKR AIIISAVLHV I LFAALIWS ...String:
MGHHHHHHHH GSLQDSEVNQ EAKPEVKPEV KPETHINLKV SDGSSEIFFK IKKTTPLRRL MEAFAKRQGK EMDSLRFLYD GIRIQADQT PEDLDMEDND IIEAHREQIG GAAADYGGDI PTTENLYFQG AAADIGSVSK ATEQNDKLKR AIIISAVLHV I LFAALIWS SFDENIEASA GGGGGSSIDA VMVDSGAVVE QYKRMQSQES SAKRSDEQRK MKEQQAAEEL REKQAAEQER LK QLEKERL AAQEQKKQAE EAAKQAELKQ KQAEEAAAKA AADAKAKAEA DAKAAEEAAK KAAADAKKKA EAEAAKAAAE AQK KAEAAA AALKKKAEAA EAAAAEARKK AATEAAEKAK AEAEKKAAAE KAAADKKAAA EKAAADKKAA EKAAAEKAAA DKKA AAEKA AADKKAAAAK AAAEKAAAAK AAAEADDIFG ELSSGKNAPK TGGGAKGNNA SPAGSGNTKN NGASGADINN YAGQI KSAI ESKFYDASSY AGKTCTLRIK LAPDGMLLDI KPEGGDPALC QAALAAAKLA KIPKPPSQAV YEVFKNAPLD FKP

UniProtKB: Ubiquitin-like protein SMT3, Tol-Pal system protein TolA

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 7 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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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: 5.4
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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 470510
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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