9MGF | pdb_00009mgf

beta-barrel assembly machine from Escherichia coli in a middle state of substrate assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structures of folding intermediates on BAM show diverse substrates fold by a conserved mechanism.

Thomson, B.D.Marquez, M.D.Rawson, S.Dos Santos, T.M.A.Harrison, S.C.Kahne, D.

(2026) Proc Natl Acad Sci U S A 123: e2534936123-e2534936123

  • DOI: https://doi.org/10.1073/pnas.2534936123
  • Primary Citation Related Structures: 
    9MGE, 9MGF, 9MGG, 9P1U

  • PubMed Abstract: 

    The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multisubunit machines. In bacteria, the β-barrel assembly machine (BAM) folds over a hundred compositionally different substrates into barrels that vary greatly in size. Some larger barrels require globular proteins to plug the barrel lumen. How a single machine can assemble such different barrels is unknown. Here we report three structures representing progressively folded stages of a 16-stranded barrel engaged with BAM, as well as the structure of a late-stage folding intermediate of a 26-stranded substrate folding around its soluble lipoprotein plug on BAM. We find that BAM catalyzes folding of these substrates by a uniform mechanism in which BAM undergoes major distortions to accommodate the nascent barrel.


  • Organizational Affiliation
    • Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138.

Macromolecule Content 

  • Total Structure Weight: 263.76 kDa 
  • Atom Count: 12,080 
  • Modeled Residue Count: 1,626 
  • Deposited Residue Count: 2,389 
  • Unique protein chains: 6
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA790Escherichia coli K-12Mutation(s): 1 
Gene Names: bamAyaeTyzzNyzzYb0177JW0172
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
Explore P0A940 
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 BamB373Escherichia coli K-12Mutation(s): 0 
Gene Names: bamByfgLb2512JW2496
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
Explore P77774 
Go to UniProtKB:  P77774
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UniProt GroupP77774
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamC320Escherichia coli K-12Mutation(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
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamD226Escherichia coli K-12Mutation(s): 0 
Gene Names: bamDyfiOb2595JW2577
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
Explore P0AC02 
Go to UniProtKB:  P0AC02
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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 BamE104Escherichia coli K-12Mutation(s): 0 
Gene Names: bamEsmpAb2617JW2598
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
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA568Escherichia coli K-12Mutation(s): 1 
Gene Names: bamAyaeTyzzNyzzYb0177JW0172
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
Explore P0A940 
Go to UniProtKB:  P0A940
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A940
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 7
MoleculeChains LengthOrganismImage
Unknown peptide8Escherichia coli K-12
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI081059
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI158028

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references
  • Version 1.2: 2026-04-15
    Changes: Data collection, Database references