7AJQ

cryo-EM structure of ExbBD from Serratia Marcescens


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog.

Biou, V.Adaixo, R.J.D.Chami, M.Coureux, P.D.Laurent, B.Enguene, V.Y.N.de Amorim, G.C.Izadi-Pruneyre, N.Malosse, C.Chamot-Rooke, J.Stahlberg, H.Delepelaire, P.

(2022) Commun Biol 5: 355-355

  • DOI: https://doi.org/10.1038/s42003-022-03306-y
  • Primary Citation of Related Structures:  
    6YE4, 7AJQ

  • PubMed Abstract: 

    ExbB and ExbD are cytoplasmic membrane proteins that associate with TonB to convey the energy of the proton-motive force to outer membrane receptors in Gram-negative bacteria for iron uptake. The opportunistic pathogen Serratia marcescens (Sm) possesses both TonB and a heme-specific TonB paralog, HasB. ExbB Sm has a long periplasmic extension absent in other bacteria such as E. coli (Ec). Long ExbB's are found in several genera of Alphaproteobacteria, most often in correlation with a hasB gene. We investigated specificity determinants of ExbB Sm and HasB. We determined the cryo-EM structures of ExbB Sm and of the ExbB-ExbD Sm complex from S. marcescens. ExbB Sm alone is a stable pentamer, and its complex includes two ExbD monomers. We showed that ExbB Sm extension interacts with HasB and is involved in heme acquisition and we identified key residues in the membrane domain of ExbB Sm and ExbB Ec , essential for function and likely involved in the interaction with TonB/HasB. Our results shed light on the class of inner membrane energy machinery formed by ExbB, ExbD and HasB.


  • Organizational Affiliation

    Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, UMR 7099 CNRS, F-75005, Paris, France. valerie.biou@ibpc.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biopolymer transport protein ExbB
A, B, C, D, E
281Serratia marcescensMutation(s): 0 
Gene Names: FHU12_5200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Biopolymer transport protein ExbD
F, G
146Serratia marcescensMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for V5YUQ0 (Serratia marcescens)
Explore V5YUQ0 
Go to UniProtKB:  V5YUQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5YUQ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.0
MODEL REFINEMENTPHENIX1.17.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France11-LABX-0011

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2022-05-04
    Changes: Database references