[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis for bacterial lipoprotein relocation by the transporter LolCDE.
Journal, issue, pagesNat Struct Mol Biol, Vol. 28, Issue 4, Page 347-355, Year 2021
Publish dateMar 29, 2021
AuthorsXiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong /
PubMed AbstractLipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the ...Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the inner membrane, lipoproteins must be transported to the outer membrane through the Lol pathway mediated by the ATP-binding cassette transporter LolCDE in the inner membrane via an unknown mechanism. Here, we report cryo-EM structures of Escherichia coli LolCDE in apo, lipoprotein-bound, LolA-bound, ADP-bound and AMP-PNP-bound states at a resolution of 3.2-3.8 Å, covering the complete lipoprotein transport cycle. Mutagenesis and in vivo viability assays verify features of the structures and reveal functional residues and structural characteristics of LolCDE. The results provide insights into the mechanisms of sorting and transport of outer-membrane lipoproteins and may guide the development of novel therapies against multidrug-resistant Gram-negative bacteria.
External linksNat Struct Mol Biol / PubMed:33782615
MethodsEM (single particle)
Resolution3.2 - 4.1 Å
Structure data

11882

7arh

EMDB-11882, PDB-7arh:
LolCDE in complex with lipoprotein
Method: EM (single particle) / Resolution: 3.3 Å

11883

7ari

EMDB-11883, PDB-7ari:
LolCDE apo structure
Method: EM (single particle) / Resolution: 3.4 Å

11884

7arj

EMDB-11884, PDB-7arj:
LolCDE in complex with lipoprotein and AMPPNP complex undimerized form
Method: EM (single particle) / Resolution: 3.2 Å

11885

7ark

EMDB-11885, PDB-7ark:
LolCDE in complex with AMP-PNP in the closed NBD state
Method: EM (single particle) / Resolution: 4.1 Å

11886

7arl

EMDB-11886, PDB-7arl:
LolCDE in complex with lipoprotein and ADP
Method: EM (single particle) / Resolution: 3.2 Å

11887

7arm

EMDB-11887, PDB-7arm:
LolCDE in complex with lipoprotein and LolA
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-Z41:
(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

ChemComp-PLM:
PALMITIC ACID

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • Escherichia coli (E. coli)
  • escherichia coli (strain k12) (bacteria)
  • escherichia coli k-12 (bacteria)
  • escherichia coli bl21(de3) (bacteria)
KeywordsPROTEIN TRANSPORT / LolCDE / lipoprotein / lipoprotein transporter / lipoprotein sorting and transport / ABC transporter

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more