5MRW

Structure of the KdpFABC complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of the potassium-importing KdpFABC membrane complex.

Huang, C.S., Pedersen, B.P., Stokes, D.L.

(2017) Nature 546: 681-685

  • DOI: 10.1038/nature22970
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four-subunit potassium pump that maintains intracellular homeostasis, cel ...

    Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four-subunit potassium pump that maintains intracellular homeostasis, cell shape and turgor under conditions in which potassium is limiting. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the superfamily of potassium transporters and another pump-like subunit (KdpB) belonging to the superfamily of P-type ATPases. Although there is considerable structural and functional information about members of both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA and a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. On the basis of these observations, we propose a mechanism that repurposes protein channel architecture for active transport across biomembranes.

    Organizational Affiliation: 

    Department of Cell Biology, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase potassium-binding subunitA, E, I557Escherichia coliMutation(s): 1 
Gene Names: kdpA, b0698, JW0686
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Superfamily of K+ Transporters (SKT proteins)		Protein: 
Potassium-importing KdpFABC membrane complex
Find proteins for P03959 (Escherichia coli (strain K12))
Explore P03959 
Go to UniProtKB:  P03959
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase ATP-binding subunitB, F, J674Escherichia coliMutation(s): 0 
Gene Names: kdpB, b0697, JW0685
EC: 3.6.3.12 (PDB Primary Data), 7.2.2.6 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Superfamily of K+ Transporters (SKT proteins)		Protein: 
Potassium-importing KdpFABC membrane complex
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 LengthOrganismDetails
Potassium-transporting ATPase KdpC subunitC, G, K187Escherichia coliMutation(s): 0 
Gene Names: kdpC, JD73_10370
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Superfamily of K+ Transporters (SKT proteins)		Protein: 
Potassium-importing KdpFABC membrane complex
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 LengthOrganismDetails
Potassium-transporting ATPase KdpF subunitD, H, L27Escherichia coliMutation(s): 0 
Gene Names: kdpF, b4513, JW0687
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Superfamily of K+ Transporters (SKT proteins)		Protein: 
Potassium-importing KdpFABC membrane complex
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PX4
Query on PX4
Download CCD File 
A, E, H, I
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O		 Ligand Interaction
BOG
Query on BOG
Download CCD File 
A, B, E, I
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
K
Query on K
Download CCD File 
A, E, I
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		B,F,JL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.72α = 90
b = 166.29β = 107.41
c = 196.3γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM108043
Danish Council for Independent ResearchDenmarkDFF-4002-00052
European Research CouncilDenmark637372

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Database references
  • Version 1.3: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary