9O9X | pdb_00009o9x

ytrEF nucleotide-free conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of a Gram-positive type VII ABC transporter induced by cell wall-targeting antibiotics.

Yu, P.Krah, B.S.Orlando, M.A.Subramanian, S.Orlando, B.J.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.10.004
  • Primary Citation of Related Structures:  
    9O9X, 9O9Y

  • PubMed Abstract: 

    Bacteria utilize a variety of mechanisms to remodel the cell wall in response to environmental and antimicrobial stress. In the model organism Bacillus subtilis, the ytr operon encoding putative ATP-binding cassette (ABC) transporter(s) is highly upregulated in response to cell wall-targeting antibiotics. Here we show that the ytr operon encodes two distinct ABC transporters: YtrBCD and YtrEF. Using cryo-electron microscopy(cryo-EM), we determined the structures of YtrEF in nucleotide-free and ADP-vanadate bound states. The structures demonstrate that YtrEF adopts a type VII ABC transporter fold. Nucleotide binding induced conformational changes that propagate from the cytosolic region through the transmembrane helices to ultimately reorient the extracellular domains. Extended bacterial growth assays and suppressor mutation identification indicated that YtrEF contributes to alteration of colony morphology. These findings establish YtrEF as a type VII ABC transporter that is induced by cell wall-targeting antibiotics and a new avenue to phenotypically assess the ytr operon.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding protein YtrEA,
D [auth B]
251Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ytrEBSU30420
Membrane Entity: Yes 
UniProt
Find proteins for O34392 (Bacillus subtilis (strain 168))
Explore O34392 
Go to UniProtKB:  O34392
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34392
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 permease YtrFB [auth C],
C [auth D]
436Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ytrFBSU30410
Membrane Entity: Yes 
UniProt
Find proteins for O35005 (Bacillus subtilis (strain 168))
Explore O35005 
Go to UniProtKB:  O35005
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35005
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM146721

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references