8zoy

Cryo-EM structure of human norepinephrine transporter NET bound with norepinephrine in an inward open state at a resolution of 2.5 angstrom

Method: ELECTRON MICROSCOPY D_max: 100.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium-dependent noradrenaline transporter

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 47–617	Not recorded	Nb_BF9 × 1 LNR L-NOREPINEPHRINE × 1 CL CHLORIDE ION × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8ZOY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HFE Cryo-EM structure of human norepinephrine transporter NET in an inward-open state at resolution of 2.5 angstrom Deposited 2022-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
8HFF Cryo-EM structure of human norepinephrine transporter NET in the presence of norepinephrine in an inward-open state at resolution of 2.9 angstrom. Deposited 2022-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	LNR L-NOREPINEPHRINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
8HFG Cryo-EM structure of human norepinephrine transporter NET in the presence of dopamine in an inward-open state at resolution of 3.0 angstrom. Deposited 2022-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	LDP L-DOPAMINE × 2 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8HFI 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. Deposited 2022-11-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	DSM 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
8HFL Cryo-EM structure of human norepinephrine transporter NET in the presence of the antidepressant bupropion in an inward-open state at resolution of 3.0 angstrom. Deposited 2022-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	1XR Bupropion × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I3V Cryo-EM structure of human norepinephrine transporter NET in the presence of the antidepressant escitalopram in an inward-open state at resolution of 2.85 angstrom. Deposited 2023-01-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	68P (1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
8WGR Cryo-EM structure of inward-open state human norepinephrine transporter NET bound with antidepressant desipramine in KCl condition. Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	DSM 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE × 2 CL CHLORIDE ION × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.75 Å
8WGX Cryo-EM structure of inward-open state human norepinephrine transporter NET bound with norepinephrine in nanodisc. Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	LNR L-NOREPINEPHRINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
8WTU Cryo-EM structure of noradrenaline transporter in apo state Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 52–617（566 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8WTV Cryo-EM structure of noradrenaline transporter in complex with noradrenaline Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 52–617（566 aa）	Not recorded	NA SODIUM ION × 2 CL CHLORIDE ION × 1 E5E Noradrenaline × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8WTW Cryo-EM structure of noradrenaline transporter in complex with a x-MrlA analogue Deposited 2023-10-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–617（566 aa）	Not recorded	CL CHLORIDE ION × 1 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8WTX Cryo-EM structure of noradrenaline transporter in complex with bupropion Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 52–617（566 aa）	Not recorded	Y60 (2~{R})-2-(~{tert}-butylamino)-1-(3-chlorophenyl)propan-1-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8WTY Cryo-EM structure of noradrenaline transporter in complex with ziprasidone Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 52–617（566 aa）	Not recorded	XEF Ziprasidone × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8XB2 Structure of radafaxine-bound state of the human Norepinephrine Transporter Deposited 2023-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–617（564 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 YNT Radafaxine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
8XB3 Structural mechanism of substrate binding and inhibition of the human Norepinephrine Transporter Deposited 2023-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–617（564 aa）	Not recorded	YMN Iobenguane × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8XB4 Structure of apo state of the human Norepinephrine Transporter Deposited 2023-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–617（564 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
8Y8Z Structure of NET-Maprotiline in outward-open state Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain E 1–617（617 aa）	Not recorded	A1LX3 ~{N}-methyl-3-(1-tetracyclo[6.6.2.0^{2,7}.0^{9,14}]hexadeca-2(7),3,5,9,11,13-hexaenyl)propan-1-amine × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8Y90 Structure of NET-Nefopam in outward-open state Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain E 1–617（617 aa）	Not recorded	A1LX6 (1S)-5-methyl-1-phenyl-1,3,4,6-tetrahydro-2,5-benzoxazocine × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8Y91 Structure of NET-nomifensine in outward-open state Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain D 1–617（617 aa）	Not recorded	NA SODIUM ION × 2 CL CHLORIDE ION × 2 A1LX5 (4S)-2-methyl-4-phenyl-3,4-dihydro-1H-isoquinolin-8-amine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
8Y92 structure of NET-Atomoxetine in outward-open state Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	A1LX4 (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8Y93 Structure of NET-Amitriptyline in outward-open state Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain E 1–617（617 aa）	Not recorded	TP0 Amitriptyline × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8Y94 Structure of Apo human norepinephrine transporter NET Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain C 1–617（617 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8Y95 Structure of NET-NE in Occluded state Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain D 1–617（617 aa）	Not recorded	E5E Noradrenaline × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8YR2 Structure of NET-Nisoxetine in outward-open state Deposited 2024-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	41U nisoxetine × 2 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 NA SODIUM ION × 4 CL CHLORIDE ION × 2 CLR CHOLESTEROL × 20 A1LX7 [(2R)-2-octanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
8Z1L Cryo-EM structure of human norepinephrine transporter NET in the presence of the antidepressant atomoxetine in an outward-open state at resolution of 3.4 angstrom. Deposited 2024-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	CL CHLORIDE ION × 1 A1LX4 (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8ZP1 Cryo-EM structure of human norepinephrine transporter NET bound with reboxetine in an outward-open state at a resolution of 2.5 angstrom Deposited 2024-05-29	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 47–617（571 aa）	Not recorded	CL CHLORIDE ION × 1 A1D9Y (2~{S})-2-[(~{S})-(2-ethoxyphenoxy)-phenyl-methyl]morpholine × 1 NA SODIUM ION × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
8ZP2 Cryo-EM structure of human norepinephrine transporter NET bound with atomoxetine in an outward-open state at a resolution of 2.4 angstrom Deposited 2024-05-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 47–617（571 aa）	Not recorded	A1LX4 (3R)-N-methyl-3-(2-methylphenoxy)-3-phenyl-propan-1-amine × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
8ZPB Cryo-EM structure of human norepinephrine transporter NET bound with norepinephrine in an occluded state at a resolution of 2.6 angstrom Deposited 2024-05-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 47–617（571 aa）	Not recorded	LNR L-NOREPINEPHRINE × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9JEL The complex structure of Y510-9709 and NET determined with Cryo-EM Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	A1EBN 3-(4-chlorophenyl)-5,6-dihydro-[1,3]thiazolo[2,3-b][1,3]thiazol-4-ium × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8	Resolution 2.98 Å
9JF3 The complex structure of 0086-0043 and NET determined with Cryo-EM. Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–617（617 aa）	Not recorded	A1EBO 2-isoquinolin-2-ium-2-yl-1-phenyl-ethanone × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8	Resolution 2.87 Å
9K6X Structural and functional basis of antinociceptive action of conotoxin AoIA at the noradrenaline transporter Deposited 2024-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	A1EET [(2~{R})-3-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propyl] (9~{Z},12~{Z})-octadeca-9,12-dienoate × 2 NA SODIUM ION × 4 CL CHLORIDE ION × 2 CLR CHOLESTEROL × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
9KDA Cryo-EM structure of lipid-mediated dimer of human norepinephrine transporter NET in the presence of the antidepressant vilazodone in an inward-open state at resolution of 2.44 angstrom. Deposited 2024-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	YG7 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide × 2 CLR CHOLESTEROL × 16 A1EFM [(2~{R})-1-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-nonanoyloxy-propan-2-yl] decanoate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.44 Å
9KDH Cryo-EM structure of LIPID-mediated dimer of human norepinephrine transporter NET in the presence of Vanoxerine in an inward-open state at resolution of 2.52 angstrom Deposited 2024-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	CLR CHOLESTEROL × 14 A1D5S Vanoxerine × 2 A1EFM [(2~{R})-1-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-nonanoyloxy-propan-2-yl] decanoate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.52 Å
9KDM Cryo-EM structure of LIPID-mediated human norepinephrine transporter NET in the presence of Levomilnacipran in an inward-open state at resolution of 2.46 angstrom. Deposited 2024-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	F0F (1R,2S)-2-(aminomethyl)-N,N-diethyl-1-phenyl-cyclopropane-1-carboxamide × 2 CLR CHOLESTEROL × 16 A1EFM [(2~{R})-1-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-nonanoyloxy-propan-2-yl] decanoate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.46 Å
9KE3 Cryo-EM structure of lipid-mediated dimer of human norepinephrine transporter NET in the presence of the F3288-0031 in an inward-open state at resolution of 3.1 angstrom Deposited 2024-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–617（617 aa） Chain B 1–617（617 aa）	Not recorded	A1EFR (2~{S})-1-[2-methoxy-4-[(~{E})-prop-1-enyl]phenoxy]-3-[4-(phenylmethyl)piperazin-1-yl]propan-2-ol × 2 CLR CHOLESTEROL × 14 A1EFM [(2~{R})-1-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-3-nonanoyloxy-propan-2-yl] decanoate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å

35 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SC6A2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–571； UniProt 47–617

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8zoy
Deposition date deposition_date	2024-05-29
Structure title title	Cryo-EM structure of human norepinephrine transporter NET bound with norepinephrine in an inward open state at a resolution of 2.5 angstrom
Keywords keywords	norepinephrine transport, norepinephrine, TRANSPORT PROTEIN/IMMUNE SYSTEM, TRANSPORT PROTEIN-IMMUNE SYSTEM complex; TRANSPORT PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.69 Å
Radius of gyration Rg (electron density) rg_electron	27.77 Å
Forward intensity I(0) i0	77382800.00
Molecular weight molecular_weight	75650.0 kDa
Excluded volume excluded_volume	97070 Å³
Envelope volume envelope_volume	108750 Å³
Hydration-shell volume shell_volume	33446 Å³
Envelope diameter envelope_diameter	109.0 Å
Shell Rg shell_rg	34.39 Å
Envelope Rg envelope_rg	28.21 Å
Shape Rg shape_rg	27.77 Å
Total Rg total_rg	28.45 Å
Total atoms total_atoms	10656
Residues n_residues	666
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.8 Å
Rg (real space) rg_real	28.86 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	7.7380e+07
I(0) uncertainty (real space) i0_real_error	1.2650e+06
Rg (reciprocal space) rg_reciprocal	28.79 Å
I(0) (reciprocal space) i0_reciprocal	77380000.0000
Solution quality estimate total_estimate	0.8331
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.574
Kurtosis Kurtosis kurtosis	-0.085
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13160000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.807; Smooth: 0.939

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Sodium-dependent noradrenaline transporter
Molecular weight formula_weight	64298.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10745

APRDGDAQPRETWGKKIDFLLSVVGFAVDLANVWRFPYLCYKNGGGAFLIPYTLFLIIAGMPLFYMELALGQYNREGAATVWKICPFFKGVGYAVILIALYVGFYYNVIIAWSLYYLFSSFTLNLPWTDCGHTWNSPNCTDPKLLNGSVLGNHTKYSKYKFTPAAEFYERGVLHLHESSGIHDIGLPQWQLLLCLMVVVIVLYFSLWKGVKTSGKVVWITATLPYFVLFVLLVHGVTLPGASNGINAYLHIDFYRLKEATVWIDAATQIFFSLGAGFGVLIAFASYNKFDNNCYRDALLTSSINCITSFVSGFAIFSILGYMAHEHKVNIEDVATEGAGLVFILYPEAISTLSGSTFWAVVFFVMLLALGLDSSMGGMEAVITGLADDFQVLKRHRKLFTFGVTFSTFLLALFCITKGGIYVLTLLDTFAAGTSILFAVLMEAIGVSWFYGVDRFSNDIQQMMGFRPGLYWRLCWKFVSPAFLLFVVVVSIINFKPLTYDDYIFPPWANWVGWGIALSSMVLVPIYVIYKFLSTQGSLWERLAYGITPENEHHLVAQRDIRQFQLQHWLAI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Nb_BF9
Molecular weight formula_weight	13396.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVQLVESGGGLVQAGGSLRLSCAASGFPVTNFEMYWYRQAPGKEREWVAAIYSTGITEYADSVKGRFTISRDNSKNTVYLQMNSLKPEDTAVYYCNVKDNGAWRQNYDYWGQGTQVTVSS

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	L-NOREPINEPHRINE
Molecular weight formula_weight	169.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	612638

fit	/app/data/saxs_computation/zo/8zoy/8zoy.fit
pddf	/app/data/pr_computation/zo/8zoy/8zoy.pr.out
profile	/app/data/saxs_computation/zo/8zoy/8zoy.dat

Cryo-EM structure of human norepinephrine transporter NET bound with norepinephrine in an inward open state at a resolution of 2.5 angstrom

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium-dependent noradrenaline transporter

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)