7LC3

CryoEM Structure of KdpFABC in E1-ATP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 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

Structural basis for potassium transport in prokaryotes by KdpFABC.

Sweet, M.E.Larsen, C.Zhang, X.Schlame, M.Pedersen, B.P.Stokes, D.L.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2105195118
  • Primary Citation of Related Structures:  
    7BH1, 7LC3, 7LC6

  • PubMed Abstract: 
  • KdpFABC is an oligomeric K + transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K + transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases ...

    KdpFABC is an oligomeric K + transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K + transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryogenic electron microscopy. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC, and KdpF remain static. We observe a series of spherical densities that we assign as K + or water and which define a pathway for K + transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K + transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K + to the cytoplasm.


    Organizational Affiliation

    Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase potassium-binding subunitA557Escherichia coli K-12Mutation(s): 1 
Gene Names: kdpAb0698JW0686
Membrane Entity: Yes 
UniProt
Find proteins for P03959 (Escherichia coli (strain K12))
Explore P03959 
Go to UniProtKB:  P03959
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): 1 
Gene Names: kdpBb0697JW0685
EC: 7.2.2.6
Membrane Entity: Yes 
UniProt
Find proteins for P03960 (Escherichia coli (strain K12))
Explore P03960 
Go to UniProtKB:  P03960
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase KdpC subunitC208Escherichia 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
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9Y0 (Subject of Investigation/LOI)
Query on 9Y0

Download Ideal Coordinates CCD File 
G [auth B](2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
C39 H76 N O8 P
DVXMEPWDARXHCX-OTMQOFQLSA-N
 Ligand Interaction
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
I [auth B]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
H [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM108043
European Research Council (ERC)Denmark637372
Danish Council for Independent ResearchDenmarkDFF-8021-00161

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references