6LYR

Structure of the BAM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structures of the beta-barrel assembly machine recognizing outer membrane protein substrates.

Xiao, L.Han, L.Li, B.Zhang, M.Zhou, H.Luo, Q.Zhang, X.Huang, Y.

(2021) FASEB J 35: e21207-e21207

  • DOI: https://doi.org/10.1096/fj.202001443RR
  • Primary Citation of Related Structures:  
    6LYQ, 6LYR, 6LYS, 6LYU

  • PubMed Abstract: 

    β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery (BAM) complex, yet its precise mechanism remains elusive. Here, we report two structures of the BAM complex in detergents and in nanodisks, and two crystal structures of the BAM complex with bound substrates. Structural analysis indicates that the membrane compositions surrounding the BAM complex could modulate its overall conformations, indicating low energy barriers between different conformational states and a highly dynamic nature of the BAM complex. Importantly, structures of the BAM complex with bound substrates and the related functional analysis show that the first β-strand of the BamA β-barrel (β1 BamA ) in the BAM complex is associated with the last but not the first β-strand of a β-OMP substrate via antiparallel β-strand interactions. These observations are consistent with the β-signal hypothesis during β-OMP biogenesis, and suggest that the β1 BamA strand in the BAM complex may interact with the last β-strand of an incoming β-OMP substrate upon their release from the chaperone-bound state.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA810Escherichia coli K-12Mutation(s): 0 
Gene Names: bamAyaeTyzzNyzzYb0177JW0172
Membrane Entity: Yes 
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A940
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UniProt GroupP0A940
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamB400Escherichia coli K-12Mutation(s): 0 
Gene Names: bamByfgLb2512JW2496
Membrane Entity: Yes 
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
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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 coli K-12Mutation(s): 0 
Gene Names: bamCdapXnlpBb2477JW2462
Membrane Entity: Yes 
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12))
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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 coli K-12Mutation(s): 0 
Gene Names: bamDyfiOb2595JW2577
Membrane Entity: Yes 
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE119Escherichia coli K-12Mutation(s): 0 
Gene Names: bamEsmpAb2617JW2598
Membrane Entity: Yes 
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12))
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  • Reference Sequence

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Outer membrane protein AF [auth P]9Escherichia coli K-12Mutation(s): 0 
Gene Names: ompAcontolGtutb0957JW0940
Membrane Entity: Yes 
UniProt
Find proteins for P0A910 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A910
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UniProt GroupP0A910
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.877α = 90
b = 116.877β = 90
c = 430.255γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary