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- EMDB-60325: Cryo-EM structure of human norepinephrine transporter NET bound w... -

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Basic information

Entry
Database: EMDB / ID: EMD-60325
TitleCryo-EM structure of human norepinephrine transporter NET bound with atomoxetine in an outward-open state at a resolution of 2.4 angstrom
Map dataCryo-EM structure of human norepinephrine transporter NET bound with Atomoxetine in an outward-open state at a resolution of 2.4 angstrom
Sample
  • Complex: human norepinephrine transporter NET in complex with Nb_BB4
    • Protein or peptide: Sodium-dependent noradrenaline transporter
    • Protein or peptide: Nb_BB4
  • Ligand: (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: water
Keywordsnorepinephrine transport / norepinephrine / inhibitor / TRANSPORT PROTEIN/IMMUNE SYSTEM / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
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 / 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
Sodium:neurotransmitter symporter, noradrenaline / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium-dependent noradrenaline transporter
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsSong AL / Wu XD
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
CitationJournal: Cell Res / Year: 2024
Title: Mechanistic insights of substrate transport and inhibitor binding revealed by high-resolution structures of human norepinephrine transporter.
Authors: Ailong Song / Xudong Wu /
History
DepositionMay 29, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60325.png

Downloads & links

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Map

FileDownload / File: emd_60325.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human norepinephrine transporter NET bound with Atomoxetine in an outward-open state at a resolution of 2.4 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 280 pix.
= 257.6 Å		0.92 Å/pix.
x 280 pix.
= 257.6 Å		0.92 Å/pix.
x 280 pix.
= 257.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.7558819 - 1.1704865
Average (Standard dev.)0.00028953588 (±0.021199053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 257.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_60325_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_60325_half_map_1.map
Annotationhalfmap_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap A

Fileemd_60325_half_map_2.map
Annotationhalfmap_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human norepinephrine transporter NET in complex with Nb_BB4

EntireName: human norepinephrine transporter NET in complex with Nb_BB4
Components
  • Complex: human norepinephrine transporter NET in complex with Nb_BB4
    • Protein or peptide: Sodium-dependent noradrenaline transporter
    • Protein or peptide: Nb_BB4
  • Ligand: (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: water

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Supramolecule #1: human norepinephrine transporter NET in complex with Nb_BB4

SupramoleculeName: human norepinephrine transporter NET in complex with Nb_BB4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Sodium-dependent noradrenaline transporter

MacromoleculeName: Sodium-dependent noradrenaline transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.298641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APRDGDAQPR ETWGKKIDFL LSVVGFAVDL ANVWRFPYLC YKNGGGAFLI PYTLFLIIAG MPLFYMELAL GQYNREGAAT VWKICPFFK GVGYAVILIA LYVGFYYNVI IAWSLYYLFS SFTLNLPWTD CGHTWNSPNC TDPKLLNGSV LGNHTKYSKY K FTPAAEFY ...String:
APRDGDAQPR ETWGKKIDFL LSVVGFAVDL ANVWRFPYLC YKNGGGAFLI PYTLFLIIAG MPLFYMELAL GQYNREGAAT VWKICPFFK GVGYAVILIA LYVGFYYNVI IAWSLYYLFS SFTLNLPWTD CGHTWNSPNC TDPKLLNGSV LGNHTKYSKY K FTPAAEFY ERGVLHLHES SGIHDIGLPQ WQLLLCLMVV VIVLYFSLWK GVKTSGKVVW ITATLPYFVL FVLLVHGVTL PG ASNGINA YLHIDFYRLK EATVWIDAAT QIFFSLGAGF GVLIAFASYN KFDNNCYRDA LLTSSINCIT SFVSGFAIFS ILG YMAHEH KVNIEDVATE GAGLVFILYP EAISTLSGST FWAVVFFVML LALGLDSSMG GMEAVITGLA DDFQVLKRHR KLFT FGVTF STFLLALFCI TKGGIYVLTL LDTFAAGTSI LFAVLMEAIG VSWFYGVDRF SNDIQQMMGF RPGLYWRLCW KFVSP AFLL FVVVVSIINF KPLTYDDYIF PPWANWVGWG IALSSMVLVP IYVIYKFLST QGSLWERLAY GITPENEHHL VAQRDI RQF QLQHWLAI

UniProtKB: Sodium-dependent noradrenaline transporter

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Macromolecule #2: Nb_BB4

MacromoleculeName: Nb_BB4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.338711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQAGGSLRL SCAASGFPVY QANMYWYRQA PGKEREWVAA IQSEGRTIYA DSVKGRFTIS RDNSKNTVYL QMNSLKPED TAVYYCNVKD AGWASYQYDY WGQGTQVTVS S

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Macromolecule #3: (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine

MacromoleculeName: (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1LX4
Molecular weightTheoretical: 255.355 Da

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #6: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 73 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 634309
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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