8BMP

Cryo-EM structure of the folate-specific ECF transporter complex in MSP2N2 lipid nanodiscs bound to ATP and ADP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Expulsion mechanism of the substrate-translocating subunit in ECF transporters.

Thangaratnarajah, C.Nijland, M.Borges-Araujo, L.Jeucken, A.Rheinberger, J.Marrink, S.J.Souza, P.C.T.Paulino, C.Slotboom, D.J.

(2023) Nat Commun 14: 4484-4484

  • DOI: https://doi.org/10.1038/s41467-023-40266-1
  • Primary Citation of Related Structures:  
    8BMP, 8BMQ, 8BMR, 8BMS

  • PubMed Abstract: 

    Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.


  • Organizational Affiliation

    Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1300Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: ecfA1cbiO1Ldb0424
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBJ0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBJ0 
Go to UniProtKB:  Q1GBJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBJ0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2287Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: ecfA2cbiO2Ldb0425
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBI9 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBI9 
Go to UniProtKB:  Q1GBI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBI9
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Folate family ECF transporter S component184Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: Ldb1625
Membrane Entity: Yes 
UniProt
Find proteins for Q1G929 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1G929 
Go to UniProtKB:  Q1G929
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UniProt GroupQ1G929
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfT265Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: cbiQecfTLdb0426
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBI8 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBI8 
Go to UniProtKB:  Q1GBI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBI8
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487-000
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union847675
Netherlands Organisation for Scientific Research (NWO)Netherlands722.017.001
Netherlands Organisation for Scientific Research (NWO)Netherlands40.018.016
Netherlands Organisation for Scientific Research (NWO)Netherlands714.018.003
European Research Council (ERC)European Union812867

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection