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- PDB-6v4j: Structure of TrkH-TrkA in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 6v4j
TitleStructure of TrkH-TrkA in complex with ATP
Components
  • Potassium uptake protein TrkA
  • Trk system potassium uptake protein TrkH
KeywordsTRANSPORT PROTEIN / Ion channel
Function / homology
Function and homology information


potassium ion transmembrane transporter activity / potassium:chloride symporter activity / potassium channel activity / potassium ion transmembrane transport / potassium ion binding / nucleotide binding / integral component of plasma membrane / protein homodimerization activity / identical protein binding / plasma membrane
TrkH potassium transport family / Regulator of K+ conductance, C-terminal domain superfamily / NAD(P)-binding domain superfamily / Regulator of K+ conductance, C-terminal / Potassium uptake protein TrkA / Regulator of K+ conductance, N-terminal / Cation transporter
Potassium uptake protein TrkA / Trk system potassium uptake protein TrkH
Biological speciesVibrio parahaemolyticus serotype O3:K6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhou, M. / Zhang, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
CitationJournal: Nat Commun / Year: 2020
Title: TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential.
Authors: Hanzhi Zhang / Yaping Pan / Liya Hu / M Ashley Hudson / Katrina S Hofstetter / Zhichun Xu / Mingqiang Rong / Zhao Wang / B V Venkataram Prasad / Steve W Lockless / Wah Chiu / Ming Zhou /
Abstract: TrkH is a bacterial ion channel implicated in K uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. ...TrkH is a bacterial ion channel implicated in K uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting in an open channel conformation. Functional studies show that both the tetramer-to-dimer conversion of TrkA and the loss of constraints on TrkH are required for channel gating. In addition, deletion of TrkA in Escherichia coli depolarizes the cell, suggesting that the TrkH-TrkA complex couples changes in intracellular nucleotides to membrane potential.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Trk system potassium uptake protein TrkH
B: Trk system potassium uptake protein TrkH
C: Trk system potassium uptake protein TrkH
D: Trk system potassium uptake protein TrkH
E: Potassium uptake protein TrkA
F: Potassium uptake protein TrkA
G: Potassium uptake protein TrkA
H: Potassium uptake protein TrkA


Theoretical massNumber of molelcules
Total (without water)413,1908
Polymers413,1908
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10700 Å2
ΔGint-57 kcal/mol
Surface area150260 Å2

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Components

#1: Protein
Trk system potassium uptake protein TrkH / TrkH


Mass: 53104.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Strain: RIMD 2210633 / Gene: trkH, VP0032 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87TN7
#2: Protein
Potassium uptake protein TrkA / TrkA


Mass: 50193.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Strain: RIMD 2210633 / Gene: VP3045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87KD2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TrkH-TrkA / Type: COMPLEX / Entity ID: 1,2 / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72317 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0117983
f_angle_d1.79924443
f_dihedral_angle_d8.14810343
f_chiral_restr0.0982927
f_plane_restr0.0132991

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