5WS4

Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb5WS4/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-12-05 Released: 2017-11-15 
• Deposition Author(s): Murakami, S., Okada, U., Yamashita, E.
• Funding Organization(s): MEXT, JSPS, JST, NIBIO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.257 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii.

Okada, U., Yamashita, E., Neuberger, A., Morimoto, M., van Veen, H.W., Murakami, S.

(2017) Nat Commun 8: 1336-1336

• PubMed: 29109439 
• DOI: https://doi.org/10.1038/s41467-017-01399-2
• Primary Citation of Related Structures:  
  5GKO, 5WS4


• PubMed Abstract: 
  

  The MacA-MacB-TolC tripartite complex is a transmembrane machine that spans both plasma membrane and outer membrane and actively extrudes substrates, including macrolide antibiotics, virulence factors, peptides and cell envelope precursors. These transport activities are driven by the ATPase MacB, a member of the ATP-binding cassette (ABC) superfamily. Here, we present the crystal structure of MacB at 3.4-Å resolution. MacB forms a dimer in which each protomer contains a nucleotide-binding domain and four transmembrane helices that protrude in the periplasm into a binding domain for interaction with the membrane fusion protein MacA. MacB represents an ABC transporter in pathogenic microorganisms with unique structural features.

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Organizational Affiliation: 

Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 145.43 kDa 
• Atom Count: 9,824 
• Modelled Residue Count: 1,300 
• Deposited Residue Count: 1,342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide export ATP-binding/permease protein MacB	A, B	671	Acinetobacter baumannii	Mutation(s): 0  Gene Names: macB EC: 3.6.3 Membrane Entity: Yes
UniProt
Find proteins for A0A0D8G707 (Acinetobacter baumannii) Explore A0A0D8G707  Go to UniProtKB:  A0A0D8G707

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AT4	C [auth A], D [auth B]	5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE C10 H15 N5 O9 P2 S HCIKUKNAJRJFOW-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.257 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.652	α = 90
b = 229.652	β = 90
c = 154.584	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing
O	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Murakami, S., Okada, U., Yamashita, E.

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Funding Organization	Location	Grant Number
MEXT	Japan	--
JSPS	Japan	--
JST	Japan	--
NIBIO	Japan	--

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references