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Yorodumi- PDB-7t3o: Rat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t3o | |||||||||
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Title | Rat vesicular glutamate transporter 2 (VGLUT2) in low Cl condition | |||||||||
Components | Vesicular glutamate transporter 2 | |||||||||
Keywords | TRANSPORT PROTEIN / synaptic vesicle / neurotransmitter / glutamate transport | |||||||||
Function / homology | Function and homology information sodium:phosphate symporter activity / sodium-dependent phosphate transport / phosphate ion uniporter activity / L-glutamate uniporter activity / pericellular basket / Organic anion transporters / neurotransmitter uptake / neurotransmitter loading into synaptic vesicle / L-glutamate import / hyaloid vascular plexus regression ...sodium:phosphate symporter activity / sodium-dependent phosphate transport / phosphate ion uniporter activity / L-glutamate uniporter activity / pericellular basket / Organic anion transporters / neurotransmitter uptake / neurotransmitter loading into synaptic vesicle / L-glutamate import / hyaloid vascular plexus regression / phosphate ion transport / L-glutamate transmembrane transport / potassium:proton antiporter activity / L-glutamate transmembrane transporter activity / phosphate ion homeostasis / neurotransmitter transmembrane transporter activity / neural retina development / regulation of synapse structure or activity / monoatomic anion transport / chloride channel activity / chloride channel complex / excitatory synapse / synaptic transmission, glutamatergic / hippocampus development / synaptic vesicle membrane / synaptic vesicle / presynapse / early endosome / neuron projection / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Li, F. / Stroud, R.M. / Edwards, R.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Substrate Recognition, Directional Flux, and Allostery in a Synaptic Vesicle Glutamate Transporter Authors: Li, F. / Stroud, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t3o.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t3o.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 7t3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t3o_validation.pdf.gz | 838.3 KB | Display | wwPDB validaton report |
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Full document | 7t3o_full_validation.pdf.gz | 840.5 KB | Display | |
Data in XML | 7t3o_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 7t3o_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/7t3o ftp://data.pdbj.org/pub/pdb/validation_reports/t3/7t3o | HTTPS FTP |
-Related structure data
Related structure data | 25666MC 7t3nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 64637.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc17a6, Dnpi, Vglut2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JI12 |
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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: complex of WT VGLUT2 with a Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 5000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152461 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6V4D 6v4d Accession code: 6V4D / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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