[English] 日本語
Yorodumi
- PDB-9kpz: Structure of TolQRA complex at pH 5.4 from E.coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kpz
TitleStructure of TolQRA complex at pH 5.4 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 transporter / proton motive force / E.coli / Outer membrane / Inner membrane
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
1,2-Distearoyl-sn-glycerophosphoethanolamine / 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: 3.18 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 5.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,39719
Polymers452,16012
Non-polymers5,2367
Water00
1


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

-
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
#4: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tol-Pal system complex TolQRA at pH 5.4 from E. coli / Type: COMPLEX / Entity ID: #1-#3 / 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: 5.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 470510 / Symmetry type: POINT
RefinementHighest resolution: 3.18 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310646
ELECTRON MICROSCOPYf_angle_d0.57714325
ELECTRON MICROSCOPYf_dihedral_angle_d15.7661613
ELECTRON MICROSCOPYf_chiral_restr0.0351650
ELECTRON MICROSCOPYf_plane_restr0.0041770

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more