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Yorodumi- EMDB-38209: Structural mechanism of substrate binding and inhibition of the h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38209 | |||||||||
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Title | Structural mechanism of substrate binding and inhibition of the human Norepinephrine Transporter | |||||||||
Map data | ||||||||||
Sample |
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Keywords | meta-iodobenzylguanidine / Radafaxin / neuroendocrine tumors / antidepression / 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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Ji WM / Wu JX | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38209.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-38209-v30.xml emd-38209.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38209_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_38209.png | 93.1 KB | ||
Masks | emd_38209_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-38209.cif.gz | 6.2 KB | ||
Others | emd_38209_half_map_1.map.gz emd_38209_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38209 | HTTPS FTP |
-Validation report
Summary document | emd_38209_validation.pdf.gz | 880.2 KB | Display | EMDB validaton report |
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Full document | emd_38209_full_validation.pdf.gz | 879.8 KB | Display | |
Data in XML | emd_38209_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_38209_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38209 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38209 | HTTPS FTP |
-Related structure data
Related structure data | 8xb3MC 8xb2C 8xb4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38209.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38209_msk_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_38209_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38209_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Homo sapiens (human) |
-Macromolecule #1: GFP-MBP-solute carrier family 6 member 2
Macromolecule | Name: GFP-MBP-solute carrier family 6 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 138.697016 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR ...String: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR HNVEGSGHHH HHHHHADRKA AVSHWQQSSG LVPRGSGWSH PQFEKGSGDY KDDDDKGSGW SHPQFEKGSG DG SVQLADH YQQNTPIGDG PVLLPDNHYL STQTKLSKDP NEKRDHMVLH EYVNAAGITG SMKIEEGKLV IWINGDKGYN GLA EVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNG KLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA LMFNLQEPYF TWPLIAADGG YAFKYENGKY DIKDV GVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGV LSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDKPLGAVAL KSYEEELVKD PRIAATMENA QKGEIMPNIP QMSAFWY AV RTAVINAASG RQTVDEALKD AQTGGLEVLF QGPEFQPRET WGKKIDFLLS VVGFAVDLAN VWRFPYLCYK NGGGAFLI P YTLFLIIAGM PLFYMELALG QYNREGAATV WKICPFFKGV GYAVILIALY VGFYYNVIIA WSLYYLFSSF TLNLPWTDC GHTWNSPNCT DPKLGGVAMP GAEDDVVGYS KYKFTPAAEF YERGVLHLHE SSGIHDIGLP QWQLLLCLMV VVIVLYFSLW KGVKTSGKV VWITATLPYF VLFVLLVHGV TLPGASNGIN AYLHIDFYRL KEATVWIDAA TQIFFSLGAG FGVLIAFASY N KFDNNCYR DALLTSSINC ITSFVSGFAI FSILGYMAHE HKVNIEDVAT EGAGLVFILY PEAISTLSGS TFWAVVFFVM LL ALGLDSS MGGMEAVITG LADDFQVLKR HRKLFTFGVT FSTFLLALFC ITKGGIYVLT LLDTFAAGTS ILFAVLMEAI GVS WFYGVD RFSNDIQQMM GFRPGLYWRL CWKFVSPAFL LFVVVVSIIN FKPLTYDDYI FPPWANWVGW GIALSSMVLV PIYV IYKFL STQGSLWERL AYGITPENEH HLVAQRDIRQ FQLQHWLAI UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Sodium-dependent noradrenaline transporter |
-Macromolecule #2: 1-[(3-iodanylphenyl)methyl]guanidine
Macromolecule | Name: 1-[(3-iodanylphenyl)methyl]guanidine / type: ligand / ID: 2 / Number of copies: 1 / Formula: YMN |
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Molecular weight | Theoretical: 275.09 Da |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |