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 

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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
  • Primary Citation of Related Structures:  
    5MRW

  • 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, cell shape and turgor under conditions in which potassium is limiting ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase potassium-binding subunitA, E, I557Escherichia coliMutation(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 subunitB, F, J674Escherichia coliMutation(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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium-transporting ATPase KdpC subunitC, G, K187Escherichia coliMutation(s): 0 
Gene Names: kdpCJD73_10370
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 subunitD, H, L27Escherichia coliMutation(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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PX4 (Subject of Investigation/LOI)
Query on PX4

Download Ideal Coordinates CCD File 
N [auth A], O [auth A], S [auth E], U [auth H], W [auth I], X [auth I]1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
BOG (Subject of Investigation/LOI)
Query on BOG

Download Ideal Coordinates CCD File 
P [auth A], Q [auth B], T [auth E], Y [auth I]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
M [auth A], R [auth E], V [auth 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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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  (Full details and data files)

  • 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