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- PDB-6v4k: Structure of TrkH-TrkA in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6v4k
TitleStructure of TrkH-TrkA in complex with ADP
Components
  • Potassium transporter peripheral membrane component
  • Trk system potassium uptake protein
KeywordsTRANSPORT PROTEIN / ion channel / TrkH / TrkA / nucleotide binding
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 / metal ion binding / identical protein 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 / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain ...Potassium uptake protein TrkA / TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, C-terminal domain / : / 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. / Regulator of K+ conductance, N-terminal / 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
ADENOSINE-5'-DIPHOSPHATE / Trk system potassium uptake protein TrkA / Trk system potassium uptake protein / Trk system potassium uptake protein TrkA / Trk system potassium uptake protein TrkH
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53004144504 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trk system potassium uptake protein
B: Trk system potassium uptake protein
C: Trk system potassium uptake protein
D: Trk system potassium uptake protein
E: Potassium transporter peripheral membrane component
F: Potassium transporter peripheral membrane component
G: Potassium transporter peripheral membrane component
H: Potassium transporter peripheral membrane component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,89912
Polymers413,1908
Non-polymers1,7094
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24520 Å2
ΔGint-127 kcal/mol
Surface area150100 Å2
Unit cell
Length a, b, c (Å)262.101, 188.495, 187.911
Angle α, β, γ (deg.)90.000, 133.163, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Trk system potassium uptake protein / TrkH


Mass: 53104.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: ACS91_07345, BA740_20060, BS585_02545, C1S91_23870, C9I78_16125, CA163_10465, CGH73_23020, CGJ02_21120, FHP20_22005, WR32_21470
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D1QU68, UniProt: Q87TN7*PLUS
#2: Protein
Potassium transporter peripheral membrane component / Trk system potassium transport protein TrkA / Trk system potassium transporter TrkA


Mass: 50193.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: trkA, sapG, ACS91_07035, BA740_20405, C1S91_23530, CGH73_23350, CGJ02_20785, WR32_21780
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072LGS4, UniProt: Q87KD2*PLUS
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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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: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 100 mM HEPES, pH 7.2, 26% PEG400, 10% 2-propanol

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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: Jul 30, 2017
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: 3.5→50 Å / Num. obs: 81759 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.3655473934 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 30.63
Reflection shellResolution: 3.52→3.58 Å / Rmerge(I) obs: 1.7 / Num. unique obs: 4081

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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: 3.53004144504→49.8219581438 Å / SU ML: 0.370948467346 / Cross valid method: FREE R-VALUE / σ(F): 1.33788131981 / Phase error: 27.9833370918
RfactorNum. reflection% reflection
Rfree0.291089168135 3403 4.93932884347 %
Rwork0.250161637564 --
obs0.252157814466 68896 84.3104861901 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.3680566079 Å2
Refinement stepCycle: LAST / Resolution: 3.53004144504→49.8219581438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28126 0 108 0 28234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045422674995928844
X-RAY DIFFRACTIONf_angle_d1.0087535857439261
X-RAY DIFFRACTIONf_chiral_restr0.09904376370984646
X-RAY DIFFRACTIONf_plane_restr0.007480485454834955
X-RAY DIFFRACTIONf_dihedral_angle_d20.137992328510171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.54-3.58050.375989872566100.315155377211242X-RAY DIFFRACTION7.43801652893
3.5805-3.63390.399256650723420.308007471372811X-RAY DIFFRACTION25.0882352941
3.6339-3.69070.359500958597850.2854664023251214X-RAY DIFFRACTION38.2847038019
3.6907-3.75110.331163866885690.2739685259921646X-RAY DIFFRACTION50.3967087864
3.7511-3.81580.263462208414910.2825278221291905X-RAY DIFFRACTION59.5110316041
3.8158-3.88520.2781093948811270.2820802542662344X-RAY DIFFRACTION73.1497927768
3.8852-3.95990.3330976335711360.2724561267222791X-RAY DIFFRACTION85.5597778427
3.9599-4.04060.3152667660791490.2577372296113045X-RAY DIFFRACTION94.3017419545
4.0406-4.12850.3150650435761440.2558857561793192X-RAY DIFFRACTION98.7859046491
4.1285-4.22450.2764583413821290.2351544936573276X-RAY DIFFRACTION99.7656021096
4.2245-4.330.2996451249851780.2340742547153192X-RAY DIFFRACTION99.8222748815
4.33-4.4470.2893713365391920.2178376193493219X-RAY DIFFRACTION99.8536299766
4.447-4.57780.2548902115091620.2102158352913229X-RAY DIFFRACTION99.7059688327
4.5778-4.72550.256492216871320.2069982088983249X-RAY DIFFRACTION99.4119376654
4.7255-4.89420.2356660423821740.2105783649463196X-RAY DIFFRACTION98.6245244366
4.8942-5.090.2174786999421520.219446711883150X-RAY DIFFRACTION97.6345357776
5.09-5.32140.2742907068331580.2392406382813244X-RAY DIFFRACTION99.8825601879
5.3214-5.60160.3029419521962100.2618783121833191X-RAY DIFFRACTION99.8825256975
5.6016-5.9520.3131487282031940.2957409897763228X-RAY DIFFRACTION99.795858851
5.952-6.41070.3072613839712040.292878115743190X-RAY DIFFRACTION99.5892018779
6.4107-7.05420.3567490069771750.278003971723210X-RAY DIFFRACTION99.5295501323
7.0542-8.07130.3230721962511810.2619954294373199X-RAY DIFFRACTION98.3415769566

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