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- PDB-6v4l: Structure of TrkH-TrkA in complex with ATPgammaS -

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Basic information

Entry
Database: PDB / ID: 6v4l
TitleStructure of TrkH-TrkA in complex with ATPgammaS
Components
  • Potassium uptake protein TrkA
  • Trk system potassium uptake protein TrkH
KeywordsTRANSPORT PROTEIN / Ion channel
Function / homology
Function and homology information


potassium:chloride symporter activity / potassium ion transmembrane transporter activity / potassium ion binding / potassium channel activity / potassium ion transmembrane transport / nucleotide binding / protein homodimerization activity / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Potassium uptake protein TrkA / TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily ...Potassium uptake protein TrkA / TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Trk system potassium uptake protein TrkA / Trk system potassium uptake protein TrkH
Similarity search - Component
Biological speciesVibrio parahaemolyticus serotype O3:K6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trk system potassium uptake protein TrkH
B: Trk system potassium uptake protein TrkH
C: Potassium uptake protein TrkA
D: Potassium uptake protein TrkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,6888
Polymers206,5954
Non-polymers2,0934
Water00
1
A: Trk system potassium uptake protein TrkH
B: Trk system potassium uptake protein TrkH
C: Potassium uptake protein TrkA
D: Potassium uptake protein TrkA
hetero molecules

A: Trk system potassium uptake protein TrkH
B: Trk system potassium uptake protein TrkH
C: Potassium uptake protein TrkA
D: Potassium uptake protein TrkA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,37616
Polymers413,1908
Non-polymers4,1868
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)164.271, 164.271, 123.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z

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Components

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


Mass: 53104.375 Da / Num. of mol.: 2
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.: 2
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
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 50 mM magnesium chloride, 50 mM ammonium phosphate monobasic, 100 mM HEPES, pH 7.3, 20% PEG400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2019
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.78→49.33 Å / Num. obs: 32522 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 1.1227169137 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 38.9
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 1.56 / Num. unique obs: 1609

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4J9U

4j9u


Resolution: 3.8→49.3285577169 Å / SU ML: 0.394599722813 / Cross valid method: THROUGHOUT / σ(F): 1.34371161272 / Phase error: 30.5130110791
RfactorNum. reflection% reflection
Rfree0.298207837322 1562 4.96787736149 %
Rwork0.25440731329 --
obs0.256616776797 31442 96.7356859367 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.2009467284 Å2
Refinement stepCycle: LAST / Resolution: 3.8→49.3285577169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14213 0 124 0 14337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048321353937114650
X-RAY DIFFRACTIONf_angle_d0.93813727502119957
X-RAY DIFFRACTIONf_chiral_restr0.05499015450772361
X-RAY DIFFRACTIONf_plane_restr0.005336307372262507
X-RAY DIFFRACTIONf_dihedral_angle_d6.330947638278565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.92210.399300121855890.2953624246511825X-RAY DIFFRACTION65.7958061189
3.9221-4.06230.287582569691540.2651876888342763X-RAY DIFFRACTION99.1502379334
4.0623-4.22480.2806015493091460.2413605883132816X-RAY DIFFRACTION100
4.2248-4.4170.2917150689791620.2294122101122770X-RAY DIFFRACTION99.9318336742
4.417-4.64970.2964895657621500.2215757515092801X-RAY DIFFRACTION100
4.6497-4.94080.2832157453441440.2236699789552781X-RAY DIFFRACTION100
4.9408-5.32180.2803105066391280.2367674016422829X-RAY DIFFRACTION99.7638326586
5.3218-5.85660.3318584688751830.2809275640662778X-RAY DIFFRACTION100
5.8566-6.70230.3250838849581340.2855860815662807X-RAY DIFFRACTION99.9660095173
6.7023-8.43730.2581616927271250.2695474735962841X-RAY DIFFRACTION100
8.4373-49.3270.2860207549171470.286681205262869X-RAY DIFFRACTION99.0151017728

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