[English] 日本語
Yorodumi
- PDB-7v8l: LolCDE with bound RcsF in nanodiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v8l
TitleLolCDE with bound RcsF in nanodiscs
Components
  • Lipoprotein-releasing system ATP-binding protein LolD
  • Lipoprotein-releasing system transmembrane protein LolC
  • Lipoprotein-releasing system transmembrane protein LolE
  • Outer membrane lipoprotein RcsF
KeywordsMEMBRANE PROTEIN / ABC transporter / lipoprotein
Function / homology
Function and homology information


positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / lipoprotein releasing activity / outer membrane protein complex / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / cellular response to cell envelope stress ...positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / lipoprotein releasing activity / outer membrane protein complex / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / cellular response to cell envelope stress / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane / transmembrane transport / outer membrane-bounded periplasmic space / intracellular signal transduction / signal transduction / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Outer membrane lipoprotein RcsF / RcsF lipoprotein / Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD ...Outer membrane lipoprotein RcsF / RcsF lipoprotein / Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-PCJ / Lipoprotein-releasing system transmembrane protein LolC / Outer membrane lipoprotein RcsF / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBei, W.W. / Luo, Q.S. / Shi, H.G. / Zhang, X.Z. / Huang, Y.H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Chinese Academy of SciencesXDB37020201 China
National Natural Science Foundation of China (NSFC)31625009 China
CitationJournal: PLoS Biol / Year: 2022
Title: Cryo-EM structures of LolCDE reveal the molecular mechanism of bacterial lipoprotein sorting in Escherichia coli.
Authors: Weiwei Bei / Qingshan Luo / Huigang Shi / Haizhen Zhou / Min Zhou / Xinzheng Zhang / Yihua Huang /
Abstract: Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe-host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer ...Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe-host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer membrane (OM) via the localization of lipoproteins (Lol) export pathway. The ATP-binding cassette (ABC) transporter LolCDE initiates the Lol pathway by selectively extracting and transporting lipoproteins for trafficking. Here, we report cryo-EM structures of LolCDE in apo, lipoprotein-bound, and AMPPNP-bound states at a resolution of 3.5 to 4.2 Å. Structure-based disulfide crosslinking, photo-crosslinking, and functional complementation assay verify the apo-state structure and reveal the molecular details regarding substrate selectivity and substrate entry route. Our studies snapshot 3 functional states of LolCDE in a transport cycle, providing deep insights into the mechanisms that underlie LolCDE-mediated lipoprotein sorting in E. coli.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Lipoprotein-releasing system transmembrane protein LolE
A: Outer membrane lipoprotein RcsF
C: Lipoprotein-releasing system transmembrane protein LolC
D: Lipoprotein-releasing system ATP-binding protein LolD
F: Lipoprotein-releasing system ATP-binding protein LolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0276
Polymers152,1305
Non-polymers8961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Lipoprotein-releasing system transmembrane protein LolE


Mass: 45385.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lolE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P75958
#2: Protein Outer membrane lipoprotein RcsF


Mass: 12506.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rcsF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69411
#3: Protein Lipoprotein-releasing system transmembrane protein LolC


Mass: 43295.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lolC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADC3
#4: Protein Lipoprotein-releasing system ATP-binding protein LolD


Mass: 25471.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lolD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#5: Chemical ChemComp-PCJ / (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE


Mass: 896.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H105NO6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: LolCDE-RcsF complex in nanodiscs / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 298 K

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225933 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029492
ELECTRON MICROSCOPYf_angle_d0.57512901
ELECTRON MICROSCOPYf_dihedral_angle_d4.0431335
ELECTRON MICROSCOPYf_chiral_restr0.0431541
ELECTRON MICROSCOPYf_plane_restr0.0061664

+
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