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- EMDB-60065: Caenorhabditis elegans ACR-23 in betaine bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-60065
TitleCaenorhabditis elegans ACR-23 in betaine bound state
Map data
Sample
  • Complex: acetylcholine receptor like-23(ACR-23)
    • Protein or peptide: Betaine receptor acr-23,Soluble cytochrome b562
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: TRIMETHYL GLYCINE
  • Ligand: water
Keywordsion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Neurotransmitter receptors and postsynaptic signal transmission / excitatory extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / electron transport chain / transmembrane signaling receptor activity / postsynapse / periplasmic space / electron transfer activity ...Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Neurotransmitter receptors and postsynaptic signal transmission / excitatory extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / electron transport chain / transmembrane signaling receptor activity / postsynapse / periplasmic space / electron transfer activity / neuron projection / iron ion binding / synapse / heme binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel ...Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Betaine receptor acr-23 / Soluble cytochrome b562
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsChen QF / Liu FL / Li TY / Gong HH / Guo F / Liu S
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071202 China
National Natural Science Foundation of China (NSFC)32100129 China
CitationJournal: To Be Published
Title: Structural basis of acetylcholine receptor like-23 (ACR-23) activation by anthelmintics monepantel and betaine
Authors: Liu FL / Li TY / Gong HH / Guo F / Liu S / Chen QF
History
DepositionMay 8, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60065.png

Downloads & links

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Map

FileDownload / File: emd_60065.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 420 pix.
= 352.8 Å		0.84 Å/pix.
x 420 pix.
= 352.8 Å		0.84 Å/pix.
x 420 pix.
= 352.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.601
Minimum - Maximum-4.4263783 - 7.2921453
Average (Standard dev.)0.008612455 (±0.14459613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 352.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60065_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_60065_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 : acetylcholine receptor like-23(ACR-23)

EntireName: acetylcholine receptor like-23(ACR-23)
Components
  • Complex: acetylcholine receptor like-23(ACR-23)
    • Protein or peptide: Betaine receptor acr-23,Soluble cytochrome b562
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: TRIMETHYL GLYCINE
  • Ligand: water

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Supramolecule #1: acetylcholine receptor like-23(ACR-23)

SupramoleculeName: acetylcholine receptor like-23(ACR-23) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 67 KDa

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Macromolecule #1: Betaine receptor acr-23,Soluble cytochrome b562

MacromoleculeName: Betaine receptor acr-23,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1
Details: Residues 387-500 correspond to the bril expression tag. Residues 599-603 and 610-612 correspond to flexible linkers, residues 604-609 correspond to the thrombin cleavage site, and residues ...Details: Residues 387-500 correspond to the bril expression tag. Residues 599-603 and 610-612 correspond to flexible linkers, residues 604-609 correspond to the thrombin cleavage site, and residues 613-620 correspond to the strep ll tag.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 70.582281 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MHRIYTFLIF ISQLALGLSN NPDIPIQYEL ANNIMENYQK GLIPKVRKGS PINVTLSLQL YQIIQVNEPQ QYLLLNAWAV ERWVDQMLG WDPSEFDNET EIMARHDDIW LPDTTLYNSL EMDDSASKKL THVKLTTLGK NQGAMVELLY PTIYKISCLL N LKYFPFDT ...String:
MHRIYTFLIF ISQLALGLSN NPDIPIQYEL ANNIMENYQK GLIPKVRKGS PINVTLSLQL YQIIQVNEPQ QYLLLNAWAV ERWVDQMLG WDPSEFDNET EIMARHDDIW LPDTTLYNSL EMDDSASKKL THVKLTTLGK NQGAMVELLY PTIYKISCLL N LKYFPFDT QTCRMTFGSW SFDNSLIDYF PRTFTNGPIG LANFLENDAW SVLGTKVNRE EKKYTCCPVN YTLLHYDVVI QR KPLYYVL NLIAPTAVIT FISIIGFFTS SSVHDLRQEK ITLGITTLLS MSIMIFMVSD KMPSTSTCVP LIALFYTLMI TII SVGTLA ASSVIFVQKL GSIGNPPASK TMKWTHRIAP FVLIQMPLVM KQAYAKRAKE EKHRKRMSRK MAEAGAMADL EDNW ETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEA QAAA EQLKTTRNAY IQKYLSQTSE TFAAPMDTSF TESLHIPELN RVASSNSIQS VLKPTEIQLT PYCTRNIVEL EWDWVA AVL ERVFLIFFTI CFLFSAIGIN LYGWYIWYTE NHFLFLEGTK LVPRGSSSGW SHPQFEK

UniProtKB: Betaine receptor acr-23, Soluble cytochrome b562, Betaine receptor acr-23

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: TRIMETHYL GLYCINE

MacromoleculeName: TRIMETHYL GLYCINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: BET
Molecular weightTheoretical: 118.154 Da
Chemical component information

ChemComp-BET:
TRIMETHYL GLYCINE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 10 / 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

Concentration4.00 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 BASE (4k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 BASE (4k x 4k) / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 214366
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

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Image processing #2

Image processing ID2
Image recording ID2
Startup modelType of model: NONE

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Image processing #3

Image processing ID3
Image recording ID1
Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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