+Open data
-Basic information
Entry | Database: PDB / ID: 6v4j | |||||||||
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Title | Structure of TrkH-TrkA in complex with ATP | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Ion channel | |||||||||
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 | |||||||||
Biological species | Vibrio parahaemolyticus serotype O3:K6 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Zhou, M. / Zhang, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v4j.cif.gz | 578.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4j.ent.gz | 486.7 KB | Display | PDB format |
PDBx/mmJSON format | 6v4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v4j_validation.pdf.gz | 988.5 KB | Display | wwPDB validaton report |
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Full document | 6v4j_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6v4j_validation.xml.gz | 77.3 KB | Display | |
Data in CIF | 6v4j_validation.cif.gz | 115 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4j ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4j | HTTPS FTP |
-Related structure data
Related structure data | 21041MC 6v4kC 6v4lC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TrkH-TrkA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.4 MDa / Experimental value: NO |
Source (natural) | Organism: Vibrio parahaemolyticus RIMD 2210633 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: SerialEM / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72317 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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