YebT domain1-4

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Cryo-EM Structure of a Bacterial Lipid Transporter YebT.

Liu, C.Ma, J.Wang, J.Wang, H.W.Zhang, L.

(2020) J Mol Biol 432: 1008-1019

  • DOI: https://doi.org/10.1016/j.jmb.2019.12.008
  • Primary Citation of Related Structures:  
    6KZ3, 6KZ4

  • PubMed Abstract: 

    The outer membrane (OM) of Gram-negative bacteria is asymmetric, with lipopolysaccharides (LPSs) on the outer surface and phospholipids (PLs) on the inner surface. This unique organization of OM makes Gram-negative bacteria resistant to many toxic chemicals. How this asymmetric distribution of lipids is maintained has been studied for decades with previous reports of an Mla (Maintenance of OM Lipid Asymmetry) system to be involved. Furthermore, the OM of Gram-negative bacteria is about 20 nm away from inner membrane (IM) where the lipids are synthesized. Therefore, how nascent lipids travel across the periplasmic space and arrive at the inner surface of OM is another interesting question. YebT is a homologue of MlaD in the Mla pathway, but its role in lipid distribution of the OM and IM is largely unknown. Here we report the first high-resolution (~3.0 Å) cryo-EM structure of full-length E. coli YebT in a substrate-bound state. Our structure with details of lipid interaction indicates that YebT is a lipid transporter spanning between IM and OM. We also demonstrate the symmetry mismatch in YebT and the existence of many other conformations of YebT revealing the intrinsic dynamics of this lipid channel. And a brief discussion on possible mechanisms of lipid transport is also included.

  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intermembrane transport protein YebT
A, B, C, D, E
A, B, C, D, E, F
464Escherichia coli K-12Mutation(s): 0 
Gene Names: yebTb1834JW1823
Membrane Entity: Yes 
Find proteins for P76272 (Escherichia coli (strain K12))
Explore P76272 
Go to UniProtKB:  P76272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76272
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China--
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references