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- EMDB-62139: Structural and functional basis of antinociceptive action of cono... -

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Basic information

Entry
Database: EMDB / ID: EMD-62139
TitleStructural and functional basis of antinociceptive action of conotoxin AoIA at the noradrenaline transporter
Map data
Sample
  • Complex: Cryo-EM structure of human norepinephrine transporter NET in an outward-open state in complex with a conotoxin ArXA-B
    • Protein or peptide: Sodium-dependent noradrenaline transporter
    • Protein or peptide: conotoxin AoIA
  • Ligand: [(2~{R})-3-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propyl] (9~{Z},12~{Z})-octadeca-9,12-dienoate
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL
KeywordsComplex / 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 / neurotransmitter transmembrane transporter activity / monoamine transmembrane transporter activity / : / SLC-mediated transport of neurotransmitters ...neurotransmitter:sodium symporter activity / Defective SLC6A2 causes orthostatic intolerance (OI) / norepinephrine uptake / : / norepinephrine:sodium symporter activity / dopamine:sodium symporter activity / neurotransmitter transmembrane transporter activity / monoamine transmembrane transporter activity / : / SLC-mediated transport of neurotransmitters / response to pain / neurotransmitter transport / neuronal cell body membrane / 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 / 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) / Conus marmoreus (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsZhang H / Harald S / Oliver B / Xu EH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural and functional basis of antinociceptive action of conotoxin AoIA at the noradrenaline transporter
Authors: Zhang H / Harald S / Oliver B / Xu EH
History
DepositionOct 22, 2024-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62139.png

Downloads & links

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Map

FileDownload / File: emd_62139.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.4686477 - 2.2924833
Average (Standard dev.)-0.0006481029 (±0.059983388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62139_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62139_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 : Cryo-EM structure of human norepinephrine transporter NET in an o...

EntireName: Cryo-EM structure of human norepinephrine transporter NET in an outward-open state in complex with a conotoxin ArXA-B
Components
  • Complex: Cryo-EM structure of human norepinephrine transporter NET in an outward-open state in complex with a conotoxin ArXA-B
    • Protein or peptide: Sodium-dependent noradrenaline transporter
    • Protein or peptide: conotoxin AoIA
  • Ligand: [(2~{R})-3-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propyl] (9~{Z},12~{Z})-octadeca-9,12-dienoate
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL

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Supramolecule #1: Cryo-EM structure of human norepinephrine transporter NET in an o...

SupramoleculeName: Cryo-EM structure of human norepinephrine transporter NET in an outward-open state in complex with a conotoxin ArXA-B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: conotoxin AoIA

MacromoleculeName: conotoxin AoIA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Conus marmoreus (invertebrata)
Molecular weightTheoretical: 1.319643 KDa
SequenceString:
RCCGYKMCH(HYP) C

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Macromolecule #2: Sodium-dependent noradrenaline transporter

MacromoleculeName: Sodium-dependent noradrenaline transporter / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.715875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SGMLLARMNP QVQPENNGAD TGPEQPLRAR KTAELLVVKE RNGVQCLLAP RDGDAQPRET WGKKIDFLLS VVGFAVDLA NVWRFPYLCY KNGGGAFLIP YTLFLIIAGM PLFYMELALG QYNREGAATV WKICPFFKGV GYAVILIALY V GFYYNVII ...String:
MDYKDDDDKG SGMLLARMNP QVQPENNGAD TGPEQPLRAR KTAELLVVKE RNGVQCLLAP RDGDAQPRET WGKKIDFLLS VVGFAVDLA NVWRFPYLCY KNGGGAFLIP YTLFLIIAGM PLFYMELALG QYNREGAATV WKICPFFKGV GYAVILIALY V GFYYNVII AWSLYYLFSS FTLNLPWTDC GHTWNSPNCT DPKLLNGSVL GNHTKYSKYK FTPAAEFYER GVLHLHESSG IH DIGLPQW QLLLCLMVVV IVLYFSLWKG VKTSGKVVWI TATLPYFVLF VLLVHGVTLP GASNGINAYL HIDFYRLKEA TVW IDAATQ IFFSLGAGFG VLIAFASYNK FDNNCYRDAL LTSSINCITS FVSGFAIFSI LGYMAHEHKV NIEDVATEGA GLVF ILYPE AISTLSGSTF WAVVFFVMLL ALGLDSSMGG MEAVITGLAD DFQVLKRHRK LFTFGVTFST FLLALFCITK GGIYV LTLL DTFAAGTSIL FAVLMEAIGV SWFYGVDRFS NDIQQMMGFR PGLYWRLCWK FVSPAFLLFV VVVSIINFKP LTYDDY IFP PWANWVGWGI ALSSMVLVPI YVIYKFLSTQ GSLWERLAYG ITPENEHHLV AQRDIRQFQL QHWLAI

UniProtKB: Sodium-dependent noradrenaline transporter

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Macromolecule #3: [(2~{R})-3-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphory...

MacromoleculeName: [(2~{R})-3-[[(2~{S})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propyl] (9~{Z},12~{Z})-octadeca-9,12-dienoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1EET
Molecular weightTheoretical: 508.582 Da

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Macromolecule #4: SODIUM ION

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

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 14 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 112752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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