6HRB

Cryo-EM structure of the KdpFABC complex in an E2 inward-facing state (state 2)


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 1.1 of the entry. See complete history


Literature

Cryo-EM structures of KdpFABC suggest a K+transport mechanism via two inter-subunit half-channels.

Stock, C.Hielkema, L.Tascon, I.Wunnicke, D.Oostergetel, G.T.Azkargorta, M.Paulino, C.Hanelt, I.

(2018) Nat Commun 9: 4971-4971

  • DOI: 10.1038/s41467-018-07319-2
  • Primary Citation of Related Structures:  
    6HRA, 6HRB

  • PubMed Abstract: 
  • P-type ATPases ubiquitously pump cations across biological membranes to maintain vital ion gradients. Among those, the chimeric K + uptake system KdpFABC is unique. While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB, K + has been assumed to be transported by the channel-like subunit KdpA ...

    P-type ATPases ubiquitously pump cations across biological membranes to maintain vital ion gradients. Among those, the chimeric K + uptake system KdpFABC is unique. While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB, K + has been assumed to be transported by the channel-like subunit KdpA. A first crystal structure uncovered its overall topology, suggesting such a spatial separation of energizing and transporting units. Here, we report two cryo-EM structures of the 157 kDa, asymmetric KdpFABC complex at 3.7 Å and 4.0 Å resolution in an E1 and an E2 state, respectively. Unexpectedly, the structures suggest a translocation pathway through two half-channels along KdpA and KdpB, uniting the alternating-access mechanism of actively pumping P-type ATPases with the high affinity and selectivity of K + channels. This way, KdpFABC would function as a true chimeric complex, synergizing the best features of otherwise separately evolved transport mechanisms.


    Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany. haenelt@biochem.uni-frankfurt.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase potassium-binding subunitA557Escherichia coli K-12Mutation(s): 0 
Gene Names: kdpAb0698JW0686
Membrane Entity: Yes 
UniProt
Find proteins for P03959 (Escherichia coli (strain K12))
Explore P03959 
Go to UniProtKB:  P03959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03959
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase ATP-binding subunitB682Escherichia coli K-12Mutation(s): 0 
Gene Names: kdpBb0697JW0685
EC: 3.6.3.12 (PDB Primary Data), 7.2.2.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P03960 (Escherichia coli (strain K12))
Explore P03960 
Go to UniProtKB:  P03960
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03960
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase KdpC subunitC190Escherichia coli K-12Mutation(s): 0 
Gene Names: kdpCb0696JW0684
Membrane Entity: Yes 
UniProt
Find proteins for P03961 (Escherichia coli (strain K12))
Explore P03961 
Go to UniProtKB:  P03961
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UniProt GroupP03961
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase KdpF subunitD29Escherichia coli K-12Mutation(s): 0 
Gene Names: kdpFb4513JW0687
Membrane Entity: Yes 
UniProt
Find proteins for P36937 (Escherichia coli (strain K12))
Explore P36937 
Go to UniProtKB:  P36937
Entity Groups  
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UniProt GroupP36937
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyHA 6322/3-1
Netherlands Organisation for Scientific ResearchNetherlands722.017.001
European Research CouncilNetherlands749732

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Other