6KZ4

YebT domain 5-7


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cryo-EM Structure of a Bacterial Lipid Transporter YebT.

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

(2019) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2019.12.008
  • Primary Citation of Related Structures:  

  • 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 ch ...

    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. Electronic address: zhang-li7@mail.tsinghua.edu.cn.,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.,School of Life Sciences, Tsinghua University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Intermembrane transport protein YebT
E, F, C, D, A, B
366Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yebT
Find proteins for P76272 (Escherichia coli (strain K12))
Go to UniProtKB:  P76272
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release