[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

TitleArchitecture and conformational dynamics of the BAM-SurA holo insertase complex.
Journal, issue, pagesSci Adv, Vol. 11, Issue 14, Page eads6094, Year 2025
Publish dateApr 4, 2025
AuthorsPhilippe A Lehner / Morris Degen / Roman P Jakob / Seyed Majed Modaresi / Morgane Callon / Björn M Burmann / Timm Maier / Sebastian Hiller /
PubMed AbstractThe proper folding of outer membrane proteins in Gram-negative bacteria relies on their delivery to the β-barrel assembly machinery (BAM) complex. The mechanism by which survival protein A (SurA), ...The proper folding of outer membrane proteins in Gram-negative bacteria relies on their delivery to the β-barrel assembly machinery (BAM) complex. The mechanism by which survival protein A (SurA), the major periplasmic chaperone, facilitates this process is not well understood. We determine the structure of the holo insertase complex, where SurA binds BAM for substrate delivery. High-resolution cryo-electron microscopy structures of four different states and a three-dimensional variability analysis show that the holo insertase complex has a large motional spectrum. SurA bound to BAM can undergo a large swinging motion between two states. This motion is uncoupled from the conformational flexibility of the BamA barrel, which can open and close without affecting SurA binding. Notably, we observed conformational coupling of the SurA swing state and the carboxyl-terminal helix grip domain of BamC. Substrate delivery by SurA to BAM appears to follow a concerted motion that encodes a gated delivery pathway through the BAM accessory proteins to the membrane entry site.
External linksSci Adv / PubMed:40184469 / PubMed Central
MethodsEM (single particle)
Resolution2.73 - 3.62 Å
Structure data

52127

9hg6

EMDB-52127, PDB-9hg6:
BAM-SurA complex in the swing-in state
Method: EM (single particle) / Resolution: 2.73 Å

52128

9hg5

EMDB-52128, PDB-9hg5:
BAM-SurA complex in the swing-in state with full length BamC resolved
Method: EM (single particle) / Resolution: 2.82 Å

52129

9hg7

EMDB-52129, PDB-9hg7:
BAM-SurA complex in the swing-out state
Method: EM (single particle) / Resolution: 2.83 Å

52130

9hg8

EMDB-52130, PDB-9hg8:
BAM-SurA complex in the swing-out state with BamC resolved
Method: EM (single particle) / Resolution: 2.9 Å

52131

9hg9

EMDB-52131, PDB-9hg9:
BAM-SurA-darobactin complex in the swing-in state
Method: EM (single particle) / Resolution: 2.88 Å

52132

9hga

EMDB-52132, PDB-9hga:
BAM-SurA-darobactin complex in the swing-out state
Method: EM (single particle) / Resolution: 3.62 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • escherichia coli k-12 (bacteria)
  • photorhabdus (bacteria)
KeywordsMEMBRANE PROTEIN / insertase / outer membrane protein / chaperone / protein folding / protein complex / darobactin

+
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