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Yorodumi- PDB-8i3v: Cryo-EM structure of human norepinephrine transporter NET in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i3v | ||||||
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Title | Cryo-EM structure of human norepinephrine transporter NET in the presence of the antidepressant escitalopram in an inward-open state at resolution of 2.85 angstrom. | ||||||
Components | Sodium-dependent noradrenaline transporter | ||||||
Keywords | MEMBRANE PROTEIN / norepinephrine / NET / escitalopram / inward-open | ||||||
Function / homology | Function and homology information neurotransmitter:sodium symporter activity / Defective SLC6A2 causes orthostatic intolerance (OI) / norepinephrine uptake / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / neurotransmitter transmembrane transporter activity / monoamine transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / monoamine transport ...neurotransmitter:sodium symporter activity / Defective SLC6A2 causes orthostatic intolerance (OI) / norepinephrine uptake / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / neurotransmitter transmembrane transporter activity / monoamine transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / monoamine transport / neurotransmitter transport / dopamine uptake involved in synaptic transmission / amino acid transport / response to pain / neuronal cell body membrane / beta-tubulin binding / sodium ion transmembrane transport / alpha-tubulin binding / neuron cellular homeostasis / presynaptic membrane / actin binding / chemical synaptic transmission / response to xenobiotic stimulus / axon / cell surface / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å | ||||||
Authors | Tan, J. / Xiao, Y. / Kong, F. / Lei, J. / Yuan, Y. / Yan, C. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Molecular basis for the reuptake and inhibition of human norepinephrine transporter Authors: Tan, J. / Xiao, Y. / Kong, F. / Lei, J. / Yuan, Y. / Yan, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i3v.cif.gz | 217 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i3v.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 8i3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i3v_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8i3v_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8i3v_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 8i3v_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/8i3v ftp://data.pdbj.org/pub/pdb/validation_reports/i3/8i3v | HTTPS FTP |
-Related structure data
Related structure data | 35157MC 8hfeC 8hffC 8hfgC 8hfiC 8hflC C: citing same article (ref.) M: map data used to model this data |
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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: 69386.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A2, NAT1, NET1, SLC6A5 / Production host: Homo sapiens (human) / References: UniProt: P23975 |
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#2: Chemical | ChemComp-68P / ( |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: NET / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275449 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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