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- PDB-9kq0: Structure of TolQRA complex at pH 8.0 from E.coli -

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Basic information

Entry
Database: PDB / ID: 9kq0
TitleStructure of TolQRA complex at pH 8.0 from E.coli
Components
  • Tol-Pal system protein TolQ
  • Tol-Pal system protein TolR
  • Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
KeywordsMEMBRANE PROTEIN / TolQRA / TolQ / TolR / TolA / Tol-Pal complex / Proton motive force / proton transporter
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 K-12 (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDong, C. / Zhang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of TolQRA complex at pH 8.0 from E.coli
Authors: Dong, C. / Zhang, Z.
History
DepositionNov 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tol-Pal system protein TolQ
B: Tol-Pal system protein TolQ
C: Tol-Pal system protein TolQ
D: Tol-Pal system protein TolQ
E: Tol-Pal system protein TolQ
F: Tol-Pal system protein TolR
G: Tol-Pal system protein TolR
H: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
I: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
J: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
K: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA
L: Ubiquitin-like protein SMT3,Tol-Pal system protein TolA


Theoretical massNumber of molelcules
Total (without water)452,16012
Polymers452,16012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tol-Pal system protein TolQ


Mass: 25779.844 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MG1655 / Gene: tolQ, fii, b0737, JW0727 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0ABU9
#2: Protein Tol-Pal system protein TolR


Mass: 15398.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MG1655 / Gene: tolR, b0738, JW0728 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0ABV6
#3: Protein
Ubiquitin-like protein SMT3,Tol-Pal system protein TolA


Mass: 58492.613 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: SMT3, YDR510W, D9719.15, tolA, cim, excC, lky, b0739, JW0729
Strain: MG1655 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q12306, UniProt: P19934
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tol-Pal system complex TolQRA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Escherichia coli (strain K12) (bacteria)83333MG1655
21Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160613 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210249
ELECTRON MICROSCOPYf_angle_d0.47313869
ELECTRON MICROSCOPYf_dihedral_angle_d3.1021368
ELECTRON MICROSCOPYf_chiral_restr0.0351638
ELECTRON MICROSCOPYf_plane_restr0.0031738

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