8Z5G

Cryo-EM structure of E.coli SPFH-NfeD family protein complex QmcA-YbbJ


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Cryo-EM structure of the SPFH-NfeD family protein complex QmcA-YbbJ.

Tan, K.A.Qiao, Z.Lim, Z.Z.E.Yeo, J.Y.Yong, Y.Do, P.H.Rya, E.Gao, Y.G.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.07.022
  • Primary Citation of Related Structures:  
    8Z5G

  • PubMed Abstract: 

    The SPFH (stomatin, prohibitin, flotillin, and HflK/C) protein family is universally present and encompasses the evolutionarily conserved SPFH domain. These proteins are predominantly localized in lipid raft and implicated in various biological processes. The NfeD (nodulation formation efficiency D) protein family is often encoded in tandem with SPFH proteins, suggesting a close functional relationship. Here, we elucidate the cryoelectron microscopy (cryo-EM) structure of the Escherichia coli QmcA-YbbJ complex belonging to the SPFH and NfeD families, respectively. Our findings reveal that the QmcA-YbbJ complex forms an intricate cage-like structure composed of 26 copies of QmcA-YbbJ heterodimers. The transmembrane helices of YbbJ act as adhesive elements bridging adjacent QmcA molecules, while the oligosaccharide-binding domain of YbbJ encapsulates the SPFH domain of QmcA. Our structural study significantly contributes to understanding the functional role of the NfeD protein family and sheds light on the interplay between SPFH and NfeD family proteins.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein QmcA305Escherichia coli K-12Mutation(s): 0 
Gene Names: qmcAybbKb0489JW0478
UniProt
Find proteins for P0AA53 (Escherichia coli (strain K12))
Explore P0AA53 
Go to UniProtKB:  P0AA53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AA53
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Inner membrane protein YbbJ152Escherichia coli K-12Mutation(s): 0 
Gene Names: ybbJb0488JW5065
UniProt
Find proteins for P0AAS3 (Escherichia coli (strain K12))
Explore P0AAS3 
Go to UniProtKB:  P0AAS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAS3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references