+Open data
-Basic information
Entry | Database: PDB / ID: 6v4k | |||||||||
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Title | Structure of TrkH-TrkA in complex with ADP | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / ion channel / TrkH / TrkA / nucleotide binding | |||||||||
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 / membrane => GO:0016020 / nucleotide binding / protein homodimerization activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Vibrio parahaemolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53004144504 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v4k.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4k.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6v4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4k ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4k | HTTPS FTP |
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-Related structure data
Related structure data | 6v4jC 6v4lC 4j9uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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 (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 | 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 / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 100 mM HEPES, pH 7.2, 26% PEG400, 10% 2-propanol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2017 |
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.52→3.58 Å / Rmerge(I) obs: 1.7 / Num. unique obs: 4081 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.3680566079 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.53004144504→49.8219581438 Å
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Refine LS restraints |
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LS refinement shell |
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