[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

TitleDe novo design of semisynthetic conduction pores.
Journal, issue, pagesNat Struct Mol Biol, Year 2026
Publish dateSep 21, 2026
AuthorsLee Schnaider / A Katherine Hatstat / Alistair J Scott / Sophia K Tan / Richard G Hambley / William M Dawson / Rhys C Griffiths / Rian C Kormos / Arthur A Melo / Eric Tse / Nicholas F Polizzi / E Jayne Wallace / Gregory E Merz / William F DeGrado /
PubMed AbstractProtein pores used for molecular sensing are generally assembled from large, multi-subunit natural proteins. Their ion conductance, and thus performance in sensing applications, depends on lumen ...Protein pores used for molecular sensing are generally assembled from large, multi-subunit natural proteins. Their ion conductance, and thus performance in sensing applications, depends on lumen geometry and chemistry. Here rather than designing a new pore or relying only on mutations to a natural scaffold, we show that installing additional de novo subunits to native protein pore complexes enables large-scale architectural changes. We design de novo proteins that integrate seamlessly with CsgG, a pore widely used in sensing applications, to form 18-subunit, 315-kilodalton semisynthetic conduction pores. This required designing within a confined, nonuniform pore under ninefold symmetry and maintaining an open conducting lumen with a stable, low-noise baseline current. The complexes exhibit distinct current-voltage responses relative to the native pore, including clear rectification, while cryo-electron microscopy confirms the designed lumen architecture, establishing a strategy for modifying existing nano-assemblies with designed protein components under stringent symmetry and structural constraints.
External linksNat Struct Mol Biol / PubMed:42768128
MethodsEM (single particle)
Resolution2.57 - 2.96 Å
Structure data

71746

9pn8

EMDB-71746, PDB-9pn8:
CsgG nanopore in complex with designed CsgX1C
Method: EM (single particle) / Resolution: 2.96 Å

71747

9pn9

EMDB-71747, PDB-9pn9:
CsgG nanopore in complex with designed CsgX2
Method: EM (single particle) / Resolution: 2.68 Å

71748

9pna

EMDB-71748, PDB-9pna:
CsgG nanopore in complex with designed CsgX1
Method: EM (single particle) / Resolution: 2.61 Å

71749

9pnb

EMDB-71749, PDB-9pnb:
CsgG nanopore in complex with designed CsgX2C
Method: EM (single particle) / Resolution: 2.57 Å

Source
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN / complex / de novo design / nanopore

+
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