4K3C | pdb_00004k3c

The crystal structure of BamA from Haemophilus ducreyi lacking POTRA domains 1-3

• PDB DOI: https://doi.org/10.2210/pdb4K3C/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): [Haemophilus] ducreyi
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-04-10 Released: 2013-09-04 
• Deposition Author(s): Noinaj, N., Lukacik, P., Chang, H., Easley, N., Buchanan, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.270 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Structural insight into the biogenesis of beta-barrel membrane proteins.

Noinaj, N., Kuszak, A.J., Gumbart, J.C., Lukacik, P., Chang, H., Easley, N.C., Lithgow, T., Buchanan, S.K.

(2013) Nature 501: 385-390

• PubMed: 23995689 
• DOI: https://doi.org/10.1038/nature12521
• Primary Citation Related Structures: 
  4K3B, 4K3C


• PubMed Abstract: 
  

  β-barrel membrane proteins are essential for nutrient import, signalling, motility and survival. In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex is responsible for the biogenesis of β-barrel membrane proteins, with homologous complexes found in mitochondria and chloroplasts. Here we describe the structure of BamA, the central and essential component of the BAM complex, from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane β-barrel domain. Three structural features shed light on the mechanism by which BamA catalyses β-barrel assembly. First, the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the β-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. And third, the β-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane.

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Organizational Affiliation: 
• National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.43 kDa 
• Atom Count: 3,959 
• Modeled Residue Count: 532 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	A	532	[Haemophilus] ducreyi	Mutation(s): 0  Gene Names: D15, bamA Membrane Entity: Yes
UniProt
Find proteins for Q93PM2 (Haemophilus ducreyi) Explore Q93PM2  Go to UniProtKB:  Q93PM2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.270 (Depositor) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.779	α = 90
b = 88.162	β = 90
c = 244.454	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHENIX/AutoSOL	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX/AutoSOL	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Noinaj, N., Lukacik, P., Chang, H., Easley, N., Buchanan, S.K.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2013-10-02
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references