[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

TitleHigh-Throughput Identification and Characterization of LptDE-Binding Bicycle Peptides Using Phage Display and Cryo-EM.
Journal, issue, pagesJ Med Chem, Vol. 68, Issue 20, Page 21144-21155, Year 2025
Publish dateOct 23, 2025
AuthorsShenaz Allyjaun / Emily Dunbar / Steven W Hardwick / Sarah Newell / Finn Holding / Catherine E Rowland / Megan A St Denis / Simone Pellegrino / Gustavo Arruda Bezerra / Nikolaos Bournakas / Dimitri Y Chirgadze / Lee Cooper / Giulia Paris / Nick Lewis / Peter Brown / Michael J Skynner / Michael J Dawson / Paul Beswick / Julia Hubbard / Bert van den Berg / Hector Newman /
PubMed AbstractThe lipopolysaccharide (LPS) transport (Lpt) system in Gram-negative bacteria maintains the integrity of the asymmetric bacterial outer membrane (OM). LPS biogenesis systems are essential in most ...The lipopolysaccharide (LPS) transport (Lpt) system in Gram-negative bacteria maintains the integrity of the asymmetric bacterial outer membrane (OM). LPS biogenesis systems are essential in most Gram-negative bacteria, with LptDE responsible for the delivery of LPS to the outer leaflet of the OM. As an externally accessible, essential protein, LptDE offers a promising target for inhibitor development without the need for cellular penetration. However, there are no direct inhibitors of LptDE, and drug discovery is made challenging since it is a membrane target without a conventional active site. Here, the bicycle phage display platform was used in combination with cryogenic-electron microscopy (cryo-EM) and surface plasmon resonance to identify and map bicyclic peptide binders to LptDE (SfLptDE). Four distinct epitopes with unique bicycle molecule binding motifs were identified across the SfLptD β-barrel. This method represents a streamlined workflow for the identification and prioritization of hit molecules against LptDE.
External linksJ Med Chem / PubMed:41048016 / PubMed Central
MethodsEM (single particle)
Resolution2.35 - 2.86 Å
Structure data

52749

9i92

EMDB-52749, PDB-9i92:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 1)
Method: EM (single particle) / Resolution: 2.41 Å

52750

9i93

EMDB-52750, PDB-9i93:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 2)
Method: EM (single particle) / Resolution: 2.86 Å

52751

9i94

EMDB-52751, PDB-9i94:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 3)
Method: EM (single particle) / Resolution: 2.84 Å

52752

9i95

EMDB-52752, PDB-9i95:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 4)
Method: EM (single particle) / Resolution: 2.35 Å

52753

9i96

EMDB-52753, PDB-9i96:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 5)
Method: EM (single particle) / Resolution: 2.67 Å

52754

9i97

EMDB-52754, PDB-9i97:
Cryo-EM structure of Shigella flexneri LptDE in complex with a Bicyclic Peptide binder (Compound 12)
Method: EM (single particle) / Resolution: 2.48 Å

52755

9i98

EMDB-52755, PDB-9i98:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 13)
Method: EM (single particle) / Resolution: 2.86 Å

52896

9q8n

EMDB-52896, PDB-9q8n:
Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 16)
Method: EM (single particle) / Resolution: 2.54 Å

Chemicals

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

PDB-1i1d:
CRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P

ChemComp-KZ0:
2,4,6-tris(chloromethyl)-1,3,5-triazine

PDB-1i1e:
CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH DOXORUBICIN


ChemComp, No image

ChemComp-R06:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-PLM:
PALMITIC ACID

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

PDB-1i4o:
CRYSTAL STRUCTURE OF THE XIAP/CASPASE-7 COMPLEX

Source
  • shigella flexneri (bacteria)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN / outer membrane protein / lipid transport / Outer membrane / LPS transport

+
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