Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.04 kDa 
• Atom Count: 3762 
• Modelled Residue Count: 494 
• Deposited Residue Count: 645 
• Unique protein chains: 1

4PK1

Structure of BamB fused to a BamA POTRA domain fragment

• PDB DOI: 10.2210/pdb4PK1/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-13 Released: 2014-12-10 
• Deposition Author(s): Jansen, K.B., Sousa, M.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.281 
• R-Value Work: 0.251 

Literature

Crystal Structure of BamB Bound to a Periplasmic Domain Fragment of BamA, the Central Component of the beta-Barrel Assembly Machine.

Jansen, K.B., Baker, S.L., Sousa, M.C.

(2015) J Biol Chem 290: 2126-2136

• PubMed: 25468906 
• DOI: 10.1074/jbc.M114.584524
• Primary Citation of Related Structures:  
  4PK1


• PubMed Abstract: 
  

The β-barrel assembly machinery (BAM) mediates folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membrane of Gram-negative bacteria. BAM is a five-protein complex consisting of the β-barrel OMP BamA and lipoproteins BamB, -C, -D, and -E. High resolution structures of all the individual BAM subunits and a BamD-BamC complex have been determined. However, the overall complex architecture remains elusive. BamA is the central component of BAM and consists of a membrane-embedded β-barrel and a periplasmic domain with five polypeptide translocation-associated (POTRA) motifs thought to interact with the accessory lipoproteins. Here we report the crystal structure of a fusion between BamB and a POTRA3-5 fragment of BamA. Extended loops 13 and 17 protruding from one end of the BamB β-propeller contact the face of the POTRA3 β-sheet in BamA. The interface is stabilized by several hydrophobic contacts, a network of hydrogen bonds, and a cation-π interaction between BamA Tyr-255 and BamB Arg-195. Disruption of BamA-BamB binding by BamA Y255A and probing of the interface by disulfide bond cross-linking validate the physiological relevance of the observed interface. Furthermore, the structure is consistent with previously published mutagenesis studies. The periplasmic five-POTRA domain of BamA is flexible in solution due to hinge motions in the POTRA2-3 linker. Modeling BamB in complex with full-length BamA shows BamB binding at the POTRA2-3 hinge, suggesting a role in modulation of BamA flexibility and the conformational changes associated with OMP folding and insertion.

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Organizational Affiliation: 

From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera protein of Outer membrane protein assembly factors BamA and BamB	A	645	Escherichia coli K-12	Mutation(s): 0  Gene Names: bamA, yaeT, yzzN, yzzY, b0177, JW0172, bamB, yfgL, b2512, JW2496
UniProt
Find proteins for P77774 (Escherichia coli (strain K12)) Explore P77774  Go to UniProtKB:  P77774
Find proteins for P0A940 (Escherichia coli (strain K12)) Explore P0A940  Go to UniProtKB:  P0A940
UniProt Groups	P77774P0A940

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.281 
• R-Value Work: 0.251 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.27	α = 90
b = 91.41	β = 92.85
c = 61.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-05-13 
• Released Date: 2014-12-10 
Deposition Author(s): Jansen, K.B., Sousa, M.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI080709

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence