[English] 日本語
Yorodumi
- EMDB-21041: Structure of TrkH-TrkA in complex with ATP -

+
Open data


ID or keywords:

Loading...

-
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 / 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, N-terminal / 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, 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 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

-
Structure visualization

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

emd_21041.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 220 pix.
= 273.24 Å		1.24 Å/pix.
x 220 pix.
= 273.24 Å		1.24 Å/pix.
x 220 pix.
= 273.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.242 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more