8P97

BtuB3G3 bound to cyanocobalamin with disordered EL8


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides.

Abellon-Ruiz, J.Jana, K.Silale, A.Frey, A.M.Basle, A.Trost, M.Kleinekathofer, U.van den Berg, B.

(2023) Nat Commun 14: 4714-4714

  • DOI: https://doi.org/10.1038/s41467-023-40427-2
  • Primary Citation of Related Structures:  
    8BLW, 8BMX, 8BMY, 8BMZ, 8BN0, 8OKV, 8P97, 8P98

  • PubMed Abstract: 

    Vitamin B 12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B 12 outer membrane transporters together with a conserved array of surface-exposed B 12 -binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B 12 with high affinities. Closing of the BtuG lid following B 12 capture causes destabilisation of the bound B 12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.


  • Organizational Affiliation

    Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TonB-dependent receptor693Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_2094
UniProt
Find proteins for Q8A5Z2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A5Z2 
Go to UniProtKB:  Q8A5Z2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A5Z2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative surface layer protein355Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
UniProt
Find proteins for Q8A5Z1 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A5Z1 
Go to UniProtKB:  Q8A5Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A5Z1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CNC (Subject of Investigation/LOI)
Query on CNC

Download Ideal Coordinates CCD File 
C [auth B]CYANOCOBALAMIN
C63 H89 Co N14 O14 P
SYZBZQWSWIJYAR-UVKKECPRSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.1.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom214222/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Refinement description