+Open data
-Basic information
Entry | Database: PDB / ID: 8xb4 | ||||||
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Title | Structure of apo state of the human Norepinephrine Transporter | ||||||
Components | GFP-MBP-solute carrier family 6 member 2 | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information 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 / monoamine transport / Na+/Cl- dependent neurotransmitter transporters ...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 / monoamine transport / Na+/Cl- dependent neurotransmitter transporters / neurotransmitter transport / amino acid transport / response to pain / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / detection of maltose stimulus / maltose transport complex / beta-tubulin binding / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / alpha-tubulin binding / sodium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / neuron cellular homeostasis / presynaptic membrane / actin binding / outer membrane-bounded periplasmic space / chemical synaptic transmission / periplasmic space / response to xenobiotic stimulus / axon / DNA damage response / cell surface / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
Authors | Wu, J.X. / Ji, W.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2024 Title: Substrate binding and inhibition mechanism of norepinephrine transporter. Authors: Wenming Ji / Anran Miao / Kai Liang / Jiameng Liu / Yuhan Qi / Yue Zhou / Xinli Duan / Jixue Sun / Lipeng Lai / Jing-Xiang Wu / Abstract: Norepinephrine transporter (NET; encoded by SLC6A2) reuptakes the majority of the released noradrenaline back to the presynaptic terminals, thereby affecting the synaptic noradrenaline level. Genetic ...Norepinephrine transporter (NET; encoded by SLC6A2) reuptakes the majority of the released noradrenaline back to the presynaptic terminals, thereby affecting the synaptic noradrenaline level. Genetic mutations and dysregulation of NET are associated with a spectrum of neurological conditions in humans, making NET an important therapeutic target. However, the structure and mechanism of NET remain unclear. Here we provide cryogenic electron microscopy structures of the human NET (hNET) in three functional states-the apo state, and in states bound to the substrate meta-iodobenzylguanidine (MIBG) or the orthosteric inhibitor radafaxine. These structures were captured in an inward-facing conformation, with a tightly sealed extracellular gate and an open intracellular gate. The substrate MIBG binds at the centre of hNET. Radafaxine also occupies the substrate-binding site and might block the structural transition of hNET for inhibition. These structures provide insights into the mechanism of substrate recognition and orthosteric inhibition of hNET. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xb4.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xb4.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 8xb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xb4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8xb4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8xb4_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 8xb4_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/8xb4 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/8xb4 | HTTPS FTP |
-Related structure data
Related structure data | 38210MC 8xb2C 8xb3C 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: 138697.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria) Gene: SLC6A2, malE / Strain: K-12 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P23975 |
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#2: Sugar | ChemComp-NAG / |
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: 7.5 |
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: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.16_3549: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194295 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Details: P23975 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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