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- EMDB-21041: Structure of TrkH-TrkA in complex with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-21041
TitleStructure of TrkH-TrkA in complex with ATP
Map dataStructure of TrkH-TrkA in complex with ATP
Sample
  • Complex: TrkH-TrkA
    • Protein or peptide: Trk system potassium uptake protein TrkH
    • Protein or peptide: Potassium uptake protein TrkA
Function / homology
Function and homology information


potassium ion transmembrane transporter activity / potassium:chloride symporter activity / potassium ion binding / potassium channel activity / potassium ion transmembrane transport / nucleotide binding / protein homodimerization activity / 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, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / 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, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Trk system potassium uptake protein TrkA / Trk system potassium uptake protein TrkH
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria) / Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhou M / Zhang H
Funding support United States, 2 items
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, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
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  • Surface view colored by radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6v4j
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21041.png

Downloads & links

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Map

FileDownload / File: emd_21041.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of TrkH-TrkA in complex with ATP
Voxel sizeX=Y=Z: 1.242 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.088603795 - 0.2613028
Average (Standard dev.)0.00095609325 (±0.006012704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 273.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2421.2421.242
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z273.240273.240273.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0890.2610.001

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Supplemental data

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Sample components

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Entire : TrkH-TrkA

EntireName: TrkH-TrkA
Components
  • Complex: TrkH-TrkA
    • Protein or peptide: Trk system potassium uptake protein TrkH
    • Protein or peptide: Potassium uptake protein TrkA

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Supramolecule #1: TrkH-TrkA

SupramoleculeName: TrkH-TrkA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Trk system potassium uptake protein TrkH

MacromoleculeName: Trk system potassium uptake protein TrkH / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Strain: RIMD 2210633
Molecular weightTheoretical: 53.104375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQFRSIIRIV GLLLALFSVT MLAPALVALL YRDGAGVPFV TTFFVLLFCG AMCWFPNRRH KHELKSRDGF LIVVLFWTVL GSAGSLPFL IADNPNISVT DAFFESFSAL TTTGATVIVG LDELPKAILF YRQFLQWFGG MGIIVLAVAI LPVLGIGGMQ L YRAEIPGP ...String:
MQFRSIIRIV GLLLALFSVT MLAPALVALL YRDGAGVPFV TTFFVLLFCG AMCWFPNRRH KHELKSRDGF LIVVLFWTVL GSAGSLPFL IADNPNISVT DAFFESFSAL TTTGATVIVG LDELPKAILF YRQFLQWFGG MGIIVLAVAI LPVLGIGGMQ L YRAEIPGP VKDTKMTPRI AETAKALWYI YLSLTIACAV AFWLAGMTPF DAISHSFSTI AIGGFSTHDA SMGYFDSYAI NL ITVVFLL ISACNFTLHF AAFASGGVHP KYYWKDPEFR AFIFIQVLLF LVCFLLLLKH HSYTSPYDAF DQALFQTVSI STT AGFTTT GFADWPLFLP VLLLFSSFIG GCAGSTGGGM KVIRILLLTL QGARELKRLV HPRAVYTIKV GGSALPQRVV DAVW GFFSA YALVFVVCML GLIATGMDEL SAFSAVAATL NNLGPGLGEV ALHFGDVNDK AKWVLIVSML FGRLEIFTLL ILLTP TFWR S

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Macromolecule #2: Potassium uptake protein TrkA

MacromoleculeName: Potassium uptake protein TrkA / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Strain: RIMD 2210633
Molecular weightTheoretical: 50.193086 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIIILGAGQ VGGTLAENLV GENNDITIVD NNADRLRELQ DKYDLRVVNG HASHPDVLHE AGAQDADMLV AVTNTDETNM AACQVAFTL FNTPNRVARI RSPEYLAEKE ALFKSGAIPV DHLIAPEELV TSYIERLIQY PGALQVVSFA EQKVSLVAVK A YYGGPLVG ...String:
MKIIILGAGQ VGGTLAENLV GENNDITIVD NNADRLRELQ DKYDLRVVNG HASHPDVLHE AGAQDADMLV AVTNTDETNM AACQVAFTL FNTPNRVARI RSPEYLAEKE ALFKSGAIPV DHLIAPEELV TSYIERLIQY PGALQVVSFA EQKVSLVAVK A YYGGPLVG NALSALREHM PHIDTRVAAI FRQGRPIRPQ GTTIIEADDE VFFVAASNHI RSVMSELQRL EKPYRRIMIV GG GNIGASL AKRLEQTYSV KLIERDYQRA EKLSEQLENT IVFCGDAADQ ELLTEENIDQ VDVFIALTNE DETNIMSAML AKR MGAKKV MVLIQRGAYV DLVQGGVIDV AISPQQATIS ALLTHVRRAD IVNVSSLRRG AAEAIEAVAH GDETTSKVVG RAIG DIKLP PGTTIGAVVR GEEVLIAHDR TVIEQDDHVV MFLVDKKYVP DVEALFQPSP FFL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72317

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