4J9U

Crystal Structure of the TrkH/TrkA potassium transport complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Gating of the TrkH ion channel by its associated RCK protein TrkA.

Cao, Y.Pan, Y.Huang, H.Jin, X.Levin, E.J.Kloss, B.Zhou, M.

(2013) Nature 496: 317-322

  • DOI: https://doi.org/10.1038/nature12056
  • Primary Citation of Related Structures:  
    4J9U, 4J9V

  • PubMed Abstract: 

    TrkH belongs to a superfamily of K(+) transport proteins required for growth of bacteria in low external K(+) concentrations. The crystal structure of TrkH from Vibrio parahaemolyticus showed that TrkH resembles a K(+) channel and may have a gating mechanism substantially different from K(+) channels. TrkH assembles with TrkA, a cytosolic protein comprising two RCK (regulate the conductance of K(+)) domains, which are found in certain K(+) channels and control their gating. However, fundamental questions on whether TrkH is an ion channel and how it is regulated by TrkA remain unresolved. Here we show single-channel activity of TrkH that is upregulated by ATP via TrkA. We report two structures of the tetrameric TrkA ring, one in complex with TrkH and one in isolation, in which the ring assumes two markedly different conformations. These results suggest a mechanism for how ATP increases TrkH activity by inducing conformational changes in TrkA.


  • Organizational Affiliation

    Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, New York 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trk system potassium uptake protein TrkH
A, B, C, D
485Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: trkHVP0032
Membrane Entity: Yes 
UniProt
Find proteins for Q87TN7 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87TN7 
Go to UniProtKB:  Q87TN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87TN7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium uptake protein TrkA
E, F, G, H
458Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: VP3045
UniProt
Find proteins for Q87KD2 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87KD2 
Go to UniProtKB:  Q87KD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87KD2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TBR
Query on TBR

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
EA [auth G]
GA [auth H]
AA [auth F],
BA [auth F],
DA [auth G],
EA [auth G],
GA [auth H],
HA [auth H],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
X [auth E],
Y [auth E]
HEXATANTALUM DODECABROMIDE
Br12 Ta6
YWYIQTPPCOBSGN-UHFFFAOYSA-M
NAD
Query on NAD

Download Ideal Coordinates CCD File 
CA [auth G],
FA [auth H],
W [auth E],
Z [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
K
Query on K

Download Ideal Coordinates CCD File 
L [auth A],
O [auth B],
R [auth C],
V [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.725α = 90
b = 146.627β = 99.32
c = 163.672γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references