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- EMDB-61426: The complex structure of 0086-0043 and NET determined with Cryo-EM. -

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Basic information

Entry
Database: EMDB / ID: EMD-61426
TitleThe complex structure of 0086-0043 and NET determined with Cryo-EM.
Map data
Sample
  • Complex: The complex structure of 0086-0043 and NET determined with Cryo-EM.
    • Protein or peptide: Sodium-dependent noradrenaline transporter
  • Ligand: 2-isoquinolin-2-ium-2-yl-1-phenyl-ethanone
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordsnoradrenaline transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


neurotransmitter:sodium symporter activity / Defective SLC6A2 causes orthostatic intolerance (OI) / norepinephrine uptake / norepinephrine:sodium symporter activity / norepinephrine transport / dopamine:sodium symporter activity / neurotransmitter transmembrane transporter activity / monoamine transmembrane transporter activity / monoamine transport / SLC-mediated transport of neurotransmitters ...neurotransmitter:sodium symporter activity / Defective SLC6A2 causes orthostatic intolerance (OI) / norepinephrine uptake / norepinephrine:sodium symporter activity / norepinephrine transport / dopamine:sodium symporter activity / neurotransmitter transmembrane transporter activity / monoamine transmembrane transporter activity / monoamine transport / SLC-mediated transport of neurotransmitters / response to pain / neuronal cell body membrane / neurotransmitter transport / dopamine uptake involved in synaptic transmission / amino acid transport / alpha-tubulin binding / beta-tubulin binding / sodium ion transmembrane transport / neuron cellular homeostasis / synaptic vesicle membrane / actin binding / presynaptic membrane / chemical synaptic transmission / response to xenobiotic stimulus / axon / cell surface / metal ion binding / membrane / 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)
Methodsingle particle reconstruction / Resolution: 2.87 Å
AuthorsJia YJ / Gao B / Tan JX / Yan CY / Zhang W / Lan YY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171204 China
CitationJournal: Science / Year: 2026
Title: Deep contrastive learning enables genome-wide virtual screening.
Authors: Yinjun Jia / Bowen Gao / Jiaxin Tan / Jiqing Zheng / Xin Hong / Wenyu Zhu / Haichuan Tan / Yuan Xiao / Liping Tan / Hongyi Cai / Yanwen Huang / Zhiheng Deng / Xiangwei Wu / Yue Jin / Yafei ...Authors: Yinjun Jia / Bowen Gao / Jiaxin Tan / Jiqing Zheng / Xin Hong / Wenyu Zhu / Haichuan Tan / Yuan Xiao / Liping Tan / Hongyi Cai / Yanwen Huang / Zhiheng Deng / Xiangwei Wu / Yue Jin / Yafei Yuan / Jiekang Tian / Wei He / Weiying Ma / Yaqin Zhang / Lei Liu / Chuangye Yan / Wei Zhang / Yanyan Lan /
Abstract: Recent breakthroughs in protein structure prediction have opened new avenues for genome-wide drug discovery, yet existing virtual screening methods remain computationally prohibitive. We present ...Recent breakthroughs in protein structure prediction have opened new avenues for genome-wide drug discovery, yet existing virtual screening methods remain computationally prohibitive. We present DrugCLIP, a contrastive learning framework that achieves ultrafast and accurate virtual screening, up to 10 million times faster than docking, while consistently outperforming various baselines on in silico benchmarks. In wet-lab validations, DrugCLIP achieved a 15% hit rate for norepinephrine transporter, and structures of two identified inhibitors were determined in complex with the target protein. For thyroid hormone receptor interactor 12, a target that lacks holo structures and small-molecule binders, DrugCLIP achieved a 17.5% hit rate using only AlphaFold2-predicted structures. Finally, we released GenomeScreenDB, an open-access database providing precomputed results for ~10,000 human proteins screened against 500 million compounds, pioneering a drug discovery paradigm in the post-AlphaFold era.
History
DepositionSep 3, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61426.png

Downloads & links

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Map

FileDownload / File: emd_61426.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.14
Minimum - Maximum-3.6033297 - 5.1770964
Average (Standard dev.)0.0050941003 (±0.13389508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 207.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61426_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61426_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61426_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex structure of 0086-0043 and NET determined with Cryo-EM.

EntireName: The complex structure of 0086-0043 and NET determined with Cryo-EM.
Components
  • Complex: The complex structure of 0086-0043 and NET determined with Cryo-EM.
    • Protein or peptide: Sodium-dependent noradrenaline transporter
  • Ligand: 2-isoquinolin-2-ium-2-yl-1-phenyl-ethanone
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: The complex structure of 0086-0043 and NET determined with Cryo-EM.

SupramoleculeName: The complex structure of 0086-0043 and NET determined with Cryo-EM.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 69.386547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG KKIDFLLSVV GFAVDLANVW RFPYLCYKN GGGAFLIPYT LFLIIAGMPL FYMELALGQY NREGAATVWK ICPFFKGVGY AVILIALYVG FYYNVIIAWS L YYLFSSFT ...String:
MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG KKIDFLLSVV GFAVDLANVW RFPYLCYKN GGGAFLIPYT LFLIIAGMPL FYMELALGQY NREGAATVWK ICPFFKGVGY AVILIALYVG FYYNVIIAWS L YYLFSSFT LNLPWTDCGH TWNSPNCTDP KLLNGSVLGN HTKYSKYKFT PAAEFYERGV LHLHESSGIH DIGLPQWQLL LC LMVVVIV LYFSLWKGVK TSGKVVWITA TLPYFVLFVL LVHGVTLPGA SNGINAYLHI DFYRLKEATV WIDAATQIFF SLG AGFGVL IAFASYNKFD NNCYRDALLT SSINCITSFV SGFAIFSILG YMAHEHKVNI EDVATEGAGL VFILYPEAIS TLSG STFWA VVFFVMLLAL GLDSSMGGME AVITGLADDF QVLKRHRKLF TFGVTFSTFL LALFCITKGG IYVLTLLDTF AAGTS ILFA VLMEAIGVSW FYGVDRFSND IQQMMGFRPG LYWRLCWKFV SPAFLLFVVV VSIINFKPLT YDDYIFPPWA NWVGWG IAL SSMVLVPIYV IYKFLSTQGS LWERLAYGIT PENEHHLVAQ RDIRQFQLQH WLAI

UniProtKB: Sodium-dependent noradrenaline transporter

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Macromolecule #2: 2-isoquinolin-2-ium-2-yl-1-phenyl-ethanone

MacromoleculeName: 2-isoquinolin-2-ium-2-yl-1-phenyl-ethanone / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EBO
Molecular weightTheoretical: 248.299 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 52 / 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

Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 8

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 507000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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