9XBY | pdb_00009xby

BAM-SurA complex (P1-visible)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XBY

This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structures of the SurA-BAM complex reveal conformational changes in outer membrane protein assembly.

Miyazaki, R.Kohga, H.Matsuoka, N.Maruno, Y.Yoshimoto, W.Takahashi, Y.S.Yanto, D.H.Y.Nugraha, Y.Shigematsu, H.Shiota, T.Tsukazaki, T.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-76843-3
  • Primary Citation Related Structures: 
    24GL, 24GT, 25FQ, 9XBY, 9XFG, 9XFO

  • PubMed Abstract: 

    The outer membrane (OM) of Gram-negative bacteria acts as a permeability barrier against toxic compounds. Its integrity is maintained by various outer membrane proteins (OMPs), which are inserted into the OM by the β-barrel assembly machinery (BAM) complex. The periplasmic chaperone SurA delivers unfolded OMPs to BAM; however, the mechanism of substrate transfer remains unclear. Here, we show that the flexible P1 and P2 domains of SurA regulate the function of its Core domain and interact with BAM components, including BamE, whose interaction with the P2 domain is crucial for efficient OMP assembly. Moreover, cryo-electron microscopy reveals four distinct Escherichia coli SurA-BAM structures, suggesting dynamic domain rearrangements of SurA. Based on these findings, we propose a dynamic model in which SurA transfers substrates to BAM through multiple conformational changes, providing a unified framework for chaperone-assisted OMP biogenesis.


  • Organizational Affiliation
    • Nara Institute of Science and Technology, Ikoma, Nara, Japan. m.ryoji@naist.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 392.37 kDa 
  • Atom Count: 14,953 
  • Modeled Residue Count: 1,917 
  • Deposited Residue Count: 3,548 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chaperone SurA,Outer membrane protein assembly factor BamA
A, F
1,222Escherichia coliMutation(s): 0 
Gene Names: surAZ0062ECs0058bamAyaeTEcE24377A_0181
EC: 5.2.1.8
UniProt
Find proteins for P0ABZ8 (Escherichia coli O157:H7)
Explore P0ABZ8 
Go to UniProtKB:  P0ABZ8
Find proteins for A7ZHR7 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZHR7 
Go to UniProtKB:  A7ZHR7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABZ8A7ZHR7
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamB392Escherichia coliMutation(s): 0 
Gene Names: bamByfgLb2512JW2496
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
Explore P77774 
Go to UniProtKB:  P77774
Entity Groups
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UniProt GroupP77774
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamC344Escherichia coliMutation(s): 0 
Gene Names: bamCdapXnlpBb2477JW2462
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12))
Explore P0A903 
Go to UniProtKB:  P0A903
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UniProt GroupP0A903
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamD245Escherichia coliMutation(s): 0 
Gene Names: bamDyfiOZ3889ECs3458
UniProt
Find proteins for P0AC04 (Escherichia coli O157:H7)
Explore P0AC04 
Go to UniProtKB:  P0AC04
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UniProt GroupP0AC04
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE123Escherichia coliMutation(s): 0 
Gene Names: bamEsmpAc3139
UniProt
Find proteins for P0A938 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P0A938 
Go to UniProtKB:  P0A938
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UniProt GroupP0A938
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release