5AYW

Structure of a membrane complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 
    0.314 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.271 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 
    0.274 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins

Han, L.Zheng, J.Wang, Y.Yang, X.Liu, Y.Sun, C.Cao, B.Zhou, H.Ni, D.Lou, J.Zhao, Y.Huang, Y.

(2016) Nat Struct Mol Biol 23: 192-196

  • DOI: https://doi.org/10.1038/nsmb.3181
  • Primary Citation of Related Structures:  
    5AYW

  • PubMed Abstract: 

    In Gram-negative bacteria, the assembly of β-barrel outer-membrane proteins (OMPs) requires the β-barrel-assembly machinery (BAM) complex. We determined the crystal structure of the 200-kDa BAM complex from Escherichia coli at 3.55-Å resolution. The structure revealed that the BAM complex assembles into a hat-like shape, in which the BamA β-barrel domain forms the hat's crown embedded in the outer membrane, and its five polypeptide transport-associated (POTRA) domains interact with the four lipoproteins BamB, BamC, BamD and BamE, thus forming the hat's brim in the periplasm. The assembly of the BAM complex creates a ring-like apparatus beneath the BamA β-barrel in the periplasm and a potential substrate-exit pore located at the outer membrane-periplasm interface. The complex structure suggests that the chaperone-bound OMP substrates may feed into the chamber of the ring-like apparatus and insert into the outer membrane via the potential substrate-exit pore in an energy-independent manner.


  • 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 BamA789Escherichia 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
Entity Groups  
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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 BamB383Escherichia coli K-12Mutation(s): 0 
Gene Names: bamByfgLb2512JW2496
Membrane Entity: Yes 
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
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Go to UniProtKB:  P77774
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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 BamC56Escherichia 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 BamD226Escherichia coli K-12Mutation(s): 0 
Gene Names: bamDyfiOb2595JW2577
Membrane Entity: Yes 
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
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UniProt GroupP0AC02
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE102Escherichia coli K-12Mutation(s): 0 
Gene Names: bamEsmpAb2617JW2598
Membrane Entity: Yes 
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12))
Explore P0A937 
Go to UniProtKB:  P0A937
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UniProt GroupP0A937
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free:  0.314 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.271 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 0.274 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.428α = 90
b = 116.428β = 90
c = 434.407γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references