+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37842 | |||||||||
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Title | Cryo-EM structure of noradrenaline transporter in apo state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | protein structure / STRUCTURAL 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 / 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 / amino acid transport / response to pain / 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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Zhao Y / Hu T / Yu Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Transport and inhibition mechanisms of the human noradrenaline transporter. Authors: Hu T / Yu Z / Zhao J / Meng Y / Salomon K / Bai Q / Wei Y / Zhang J / Xu S / Dai Q / Yu R / Yang B / Loland CJ / Zhao Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37842.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-37842-v30.xml emd-37842.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_37842.png | 172.6 KB | ||
Filedesc metadata | emd-37842.cif.gz | 5.6 KB | ||
Others | emd_37842_half_map_1.map.gz emd_37842_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37842 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37842 | HTTPS FTP |
-Validation report
Summary document | emd_37842_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_37842_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_37842_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_37842_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37842 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37842 | HTTPS FTP |
-Related structure data
Related structure data | 8wtuMC 8wtvC 8wtwC 8wtxC 8wtyC 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_37842.map.gz / Format: CCP4 / Size: 125 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: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37842_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37842_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : structure of a protein
Entire | Name: structure of a protein |
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Components |
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-Supramolecule #1: structure of a protein
Supramolecule | Name: structure of a protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.8 kDa/nm |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 63.801109 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DAQPRETWGK KIDFLLSVVG FAVDLANVWR FPYLCYKNGG GAFLIPYTLF LIIAGMPLFY MELALGQYNR EGAATVWKIC PFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA A EFYERGVL ...String: DAQPRETWGK KIDFLLSVVG FAVDLANVWR FPYLCYKNGG GAFLIPYTLF LIIAGMPLFY MELALGQYNR EGAATVWKIC PFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA A EFYERGVL HLHESSGIHD IGLPQWQLLL CLMVVVIVLY FSLWKGVKTS GKVVWITATL PYFVLFVLLV HGVTLPGASN GI NAYLHID FYRLKEATVW IDAATQIFFS LGAGFGVLIA FASYNKFDNN CYRDALLTSS INCITSFVSG FAIFSILGYM AHE HKVNIE DVATEGAGLV FILYPEAIST LSGSTFWAVV FFVMLLALGL DSSMGGMEAV ITGLADDFQV LKRHRKLFTF GVTF STFLL ALFCITKGGI YVLTLLDTFA AGTSILFAVL MEAIGVSWFY GVDRFSNDIQ QMMGFRPGLY WRLCWKFVSP AFLLF VVVV SIINFKPLTY DDYIFPPWAN WVGWGIALSS MVLVPIYVIY KFLSTQGSLW ERLAYGITPE NEHHLVAQRD IRQFQL QHW LAI UniProtKB: Sodium-dependent noradrenaline transporter |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / 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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 268436 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |