4HZU

Structure of a bacterial energy-coupling factor transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a bacterial energy-coupling factor transporter.

Wang, T.Fu, G.Pan, X.Wu, J.Gong, X.Wang, J.Shi, Y.

(2013) Nature 497: 272-276

  • DOI: 10.1038/nature12045
  • Primary Citation of Related Structures:  
    4HZU

  • PubMed Abstract: 
  • The energy-coupling factor (ECF) transporters constitute a novel family of conserved membrane transporters in prokaryotes that have a similar domain organization to the ATP-binding cassette transporters. Each ECF transporter comprises a pair of cytosolic ATPases (the A and A' components, or EcfA and EcfA'), a membrane-embedded substrate-binding protein (the S component, or EcfS) and a transmembrane energy-coupling component (the T component, or EcfT) that links the EcfA-EcfA' subcomplex to EcfS ...

    The energy-coupling factor (ECF) transporters constitute a novel family of conserved membrane transporters in prokaryotes that have a similar domain organization to the ATP-binding cassette transporters. Each ECF transporter comprises a pair of cytosolic ATPases (the A and A' components, or EcfA and EcfA'), a membrane-embedded substrate-binding protein (the S component, or EcfS) and a transmembrane energy-coupling component (the T component, or EcfT) that links the EcfA-EcfA' subcomplex to EcfS. The structure and transport mechanism of the quaternary ECF transporter remain largely unknown. Here we report the crystal structure of a nucleotide-free ECF transporter from Lactobacillus brevis at a resolution of 3.5 Å. The T component has a horseshoe-shaped open architecture, with five α-helices as transmembrane segments and two cytoplasmic α-helices as coupling modules connecting to the A and A' components. Strikingly, the S component, thought to be specific for hydroxymethyl pyrimidine, lies horizontally along the lipid membrane and is bound exclusively by the five transmembrane segments and the two cytoplasmic helices of the T component. These structural features suggest a plausible working model for the transport cycle of the ECF transporters.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA 1A [auth B]290Levilactobacillus brevisMutation(s): 0 
Gene Names: ecfA1cbiO1LVIS_1661
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for Q03PY6 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03PY6 
Go to UniProtKB:  Q03PY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03PY6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA 2B [auth A]279Levilactobacillus brevisMutation(s): 0 
Gene Names: ecfA2cbiO2LVIS_1662
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q03PY5 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03PY5 
Go to UniProtKB:  Q03PY5
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UniProt GroupQ03PY5
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Energy-coupling factor transporter transmembrane protein EcfTC [auth T]266Levilactobacillus brevisMutation(s): 0 
Gene Names: ecfTLVIS_1660
Membrane Entity: Yes 
UniProt
Find proteins for Q03PY7 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
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Go to UniProtKB:  Q03PY7
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UniProt GroupQ03PY7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Predicted membrane proteinD [auth S]166Levilactobacillus brevisMutation(s): 0 
Gene Names: LVIS_2151
Membrane Entity: Yes 
UniProt
Find proteins for Q03NM0 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
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Go to UniProtKB:  Q03NM0
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UniProt GroupQ03NM0
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.971α = 90
b = 148.69β = 90
c = 154.574γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references