5XU1

Structure of a non-canonical ABC transporter from Streptococcus pneumoniae R6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a MacAB-like efflux pump from Streptococcus pneumoniae.

Yang, H.B.Hou, W.T.Cheng, M.T.Jiang, Y.L.Chen, Y.Zhou, C.Z.

(2018) Nat Commun 9: 196-196

  • DOI: https://doi.org/10.1038/s41467-017-02741-4
  • Primary Citation of Related Structures:  
    5XU0, 5XU1

  • PubMed Abstract: 

    The spr0693-spr0694-spr0695 operon of Streptococcus pneumoniae encodes a putative ATP-binding cassette (ABC)-type efflux pump involved in the resistance of antibiotics and antimicrobial peptides. Here we report the crystal structures of Spr0694-0695 at 3.3 Å and Spr0693 at 3.0 Å resolution, revealing a MacAB-like efflux pump. The dimeric Spr0694-0695 adopts a non-canonical fold of ABC transporter, the transmembrane domain of which consists of eight tightly packed transmembrane helices with an insertion of extracellular domain between the first and second helices, whereas Spr0693 forms a nanotube channel docked onto the ABC transporter. Structural analyses combined with ATPase activity and antimicrobial susceptibility assays, enable us to propose a putative substrate-entrance tunnel with a lateral access controlled by a guard helix. Altogether, our findings provide structural insights and putative transport mechanism of a MacAB-like efflux pump in Gram-positive bacteria.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding protein
A, B
245Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: ABC-NBDspr0694
UniProt
Find proteins for Q8DQF8 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQF8 
Go to UniProtKB:  Q8DQF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQF8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter permeaeC [auth M],
D [auth S]
419Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: spr0695
Membrane Entity: Yes 
UniProt
Find proteins for Q8DQF7 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQF7 
Go to UniProtKB:  Q8DQF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQF7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.053α = 90
b = 154.987β = 90
c = 205.892γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2015CB910103
National Natural Science Foundation of ChinaChina31400628

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description