5XU0 | pdb_00005xu0

Structure of the membrane fusion protein Spr0693 from Streptococcus pneumoniae R6

• PDB DOI: https://doi.org/10.2210/pdb5XU0/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-22 Released: 2018-01-24 
• Deposition Author(s): Yang, H.B., Jiang, Y.L., Hou, W.T., Chen, M.T., Chen, Y., Zhou, C.Z.
• Funding Organization(s): Ministry of Science and Technology, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.305 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.248 (Depositor) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

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

• PubMed: 29335499 
• DOI: https://doi.org/10.1038/s41467-017-02741-4
• Primary Citation 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.

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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.
Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China.
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. [e-mail].
Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China. [e-mail].
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. [e-mail].
Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China. [e-mail].
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. [e-mail].
Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 87.07 kDa 
• Atom Count: 5,102 
• Modeled Residue Count: 681 
• Deposited Residue Count: 819 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-fusion protein	A, B, C	273	Streptococcus pneumoniae	Mutation(s): 2  Gene Names: ERS515107_03100

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.305 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.248 (Depositor) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.21	α = 90
b = 159.21	β = 90
c = 99.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-24 
Deposition Author(s): Yang, H.B., Jiang, Y.L., Hou, W.T., Chen, M.T., Chen, Y., Zhou, C.Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology	China	2015CB910103
National Natural Science Foundation of China	China	31400628

Revision History  

• 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
• Version 1.3: 2024-10-30
  Changes: Structure summary