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- EMDB-34721: Cryo-EM structure of human norepinephrine transporter NET in the ... -
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Open data
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Basic information
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Title | Cryo-EM structure of human norepinephrine transporter NET in the presence of the antidepressant desipramine in an inward-open state at resolution of 2.5 angstrom. | |||||||||
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![]() | Norepinephrine transporter / NET / SLC6A2 / norepinephrine / dopamine / neurotransmitter / desipramine / bupropion / antidepressant. / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() neurotransmitter:sodium symporter activity / Defective SLC6A2 causes orthostatic intolerance (OI) / norepinephrine uptake / norepinephrine:sodium symporter activity / dopamine: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 / norepinephrine:sodium symporter activity / dopamine: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 / response to pain / amino acid transport / neuronal cell body membrane / beta-tubulin binding / alpha-tubulin binding / sodium ion transmembrane transport / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
![]() | Tan J / Xiao Y / Kong F / Lei J / Yuan Y / Yan C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of human noradrenaline transporter reuptake and inhibition. Authors: Jiaxin Tan / Yuan Xiao / Fang Kong / Xiaochun Zhang / Hanwen Xu / Angqi Zhu / Yiming Liu / Jianlin Lei / Boxue Tian / Yafei Yuan / Chuangye Yan / ![]() Abstract: Noradrenaline, also known as norepinephrine, has a wide range of activities and effects on most brain cell types. Its reuptake from the synaptic cleft heavily relies on the noradrenaline transporter ...Noradrenaline, also known as norepinephrine, has a wide range of activities and effects on most brain cell types. Its reuptake from the synaptic cleft heavily relies on the noradrenaline transporter (NET) located in the presynaptic membrane. Here we report the cryo-electron microscopy (cryo-EM) structures of the human NET in both its apo state and when bound to substrates or antidepressant drugs, with resolutions ranging from 2.5 Å to 3.5 Å. The two substrates, noradrenaline and dopamine, display a similar binding mode within the central substrate binding site (S1) and within a newly identified extracellular allosteric site (S2). Four distinct antidepressants, namely, atomoxetine, desipramine, bupropion and escitalopram, occupy the S1 site to obstruct substrate transport in distinct conformations. Moreover, a potassium ion was observed within sodium-binding site 1 in the structure of the NET bound to desipramine under the KCl condition. Complemented by structural-guided biochemical analyses, our studies reveal the mechanism of substrate recognition, the alternating access of NET, and elucidate the mode of action of the four antidepressants. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
Images | ![]() | 185.8 KB | ||
Masks | ![]() | 27 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 25.1 MB 25.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hfiMC ![]() 8hfeC ![]() 8hffC ![]() 8hfgC ![]() 8hflC ![]() 8i3vC ![]() 8wgrC ![]() 8wgxC ![]() 8z1lC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : NET
Entire | Name: NET |
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Components |
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-Supramolecule #1: NET
Supramolecule | Name: NET / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: Sodium-dependent noradrenaline transporter
Macromolecule | Name: Sodium-dependent noradrenaline transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 69.386547 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG KKIDFLLSVV GFAVDLANVW RFPYLCYKN GGGAFLIPYT LFLIIAGMPL FYMELALGQY NREGAATVWK ICPFFKGVGY AVILIALYVG FYYNVIIAWS L YYLFSSFT ...String: MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG KKIDFLLSVV GFAVDLANVW RFPYLCYKN GGGAFLIPYT LFLIIAGMPL FYMELALGQY NREGAATVWK ICPFFKGVGY AVILIALYVG FYYNVIIAWS L YYLFSSFT LNLPWTDCGH TWNSPNCTDP KLLNGSVLGN HTKYSKYKFT PAAEFYERGV LHLHESSGIH DIGLPQWQLL LC LMVVVIV LYFSLWKGVK TSGKVVWITA TLPYFVLFVL LVHGVTLPGA SNGINAYLHI DFYRLKEATV WIDAATQIFF SLG AGFGVL IAFASYNKFD NNCYRDALLT SSINCITSFV SGFAIFSILG YMAHEHKVNI EDVATEGAGL VFILYPEAIS TLSG STFWA VVFFVMLLAL GLDSSMGGME AVITGLADDF QVLKRHRKLF TFGVTFSTFL LALFCITKGG IYVLTLLDTF AAGTS ILFA VLMEAIGVSW FYGVDRFSND IQQMMGFRPG LYWRLCWKFV SPAFLLFVVV VSIINFKPLT YDDYIFPPWA NWVGWG IAL SSMVLVPIYV IYKFLSTQGS LWERLAYGIT PENEHHLVAQ RDIRQFQLQH WLAI UniProtKB: Sodium-dependent noradrenaline transporter |
-Macromolecule #2: 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE
Macromolecule | Name: 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE type: ligand / ID: 2 / Number of copies: 1 / Formula: DSM |
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Molecular weight | Theoretical: 266.381 Da |
Chemical component information | ![]() ChemComp-DSM: |
-Macromolecule #3: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 39 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 439839 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |