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- EMDB-43924: Bovine adult muscle nAChR resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-43924
TitleBovine adult muscle nAChR resting state
Map datasharp
Sample
  • Complex: Bovine muscle nicotinic acetylcholine receptor
    • Protein or peptide: Acetylcholine receptor subunit alpha
    • Protein or peptide: Acetylcholine receptor subunit beta
    • Protein or peptide: Acetylcholine receptor subunit delta
    • Protein or peptide: Acetylcholine receptor subunit epsilon
    • Protein or peptide: Toxin
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsBovine muscle nicotinic acetylcholine receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / postsynaptic membrane organization / skeletal muscle tissue growth / musculoskeletal movement / neuromuscular synaptic transmission / acetylcholine-gated channel complex / behavioral response to nicotine / muscle cell development ...Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / postsynaptic membrane organization / skeletal muscle tissue growth / musculoskeletal movement / neuromuscular synaptic transmission / acetylcholine-gated channel complex / behavioral response to nicotine / muscle cell development / acetylcholine receptor activity / synaptic transmission, cholinergic / acetylcholine binding / postsynaptic specialization membrane / acetylcholine receptor signaling pathway / nervous system process / channel activity / acetylcholine-gated monoatomic cation-selective channel activity / neuromuscular junction development / muscle cell cellular homeostasis / monoatomic cation transport / membrane depolarization / skeletal muscle contraction / neuronal action potential / muscle contraction / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nicotine / neuromuscular junction / neuron cellular homeostasis / postsynaptic membrane / neuron projection / synapse / cell surface / signal transduction / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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
Acetylcholine receptor subunit alpha / Acetylcholine receptor subunit epsilon / Acetylcholine receptor subunit beta / Acetylcholine receptor subunit delta
Similarity search - Component
Biological speciesBos taurus (cattle) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsLi H / Hibbs RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Nature / Year: 2024
Title: Structural switch in acetylcholine receptors in developing muscle
Authors: Li H / Teng JF / Hibbs RE
History
DepositionMar 5, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43924.png

Downloads & links

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Map

FileDownload / File: emd_43924.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 512 pix.
= 478.72 Å		0.94 Å/pix.
x 512 pix.
= 478.72 Å		0.94 Å/pix.
x 512 pix.
= 478.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.8042587 - 2.7858357
Average (Standard dev.)0.000075733595 (±0.052135203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 478.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharp

Fileemd_43924_additional_1.map
Annotationunsharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: EMhancer

Fileemd_43924_additional_2.map
AnnotationEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: adult resting halfmapA

Fileemd_43924_half_map_1.map
Annotationadult_resting_halfmapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: adult resting halfmapB

Fileemd_43924_half_map_2.map
Annotationadult_resting_halfmapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bovine muscle nicotinic acetylcholine receptor

EntireName: Bovine muscle nicotinic acetylcholine receptor
Components
  • Complex: Bovine muscle nicotinic acetylcholine receptor
    • Protein or peptide: Acetylcholine receptor subunit alpha
    • Protein or peptide: Acetylcholine receptor subunit beta
    • Protein or peptide: Acetylcholine receptor subunit delta
    • Protein or peptide: Acetylcholine receptor subunit epsilon
    • Protein or peptide: Toxin
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Bovine muscle nicotinic acetylcholine receptor

SupramoleculeName: Bovine muscle nicotinic acetylcholine receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Acetylcholine receptor subunit alpha

MacromoleculeName: Acetylcholine receptor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 49.949828 KDa
SequenceString: SEHETRLVAK LFEDYNSVVR PVEDHRQAVE VTVGLQLIQL INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPD LVLYNNADGD FAIVKFTKVL LDYTGHITWT PPAIFKSYCE IIVTHFPFDE QNCSMKLGTW TYDGSVVVIN P ESDQPDLS ...String:
SEHETRLVAK LFEDYNSVVR PVEDHRQAVE VTVGLQLIQL INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPD LVLYNNADGD FAIVKFTKVL LDYTGHITWT PPAIFKSYCE IIVTHFPFDE QNCSMKLGTW TYDGSVVVIN P ESDQPDLS NFMESGEWVI KESRGWKHWV FYACCPSTPY LDITYHFVMQ RLPLYFIVNV IIPCLLFSFL TGLVFYLPTD SG EKMTLSI SVLLSLTVFL LVIVELIPST SSAVPLIGKY MLFTMVFVIA SIIITVIVIN THHRSPSTHV MPEWVRKVFI DTI PNIMFF STMKRPSREK QDKKIFTEDI DISDISGKPG PPPMGFHSPL IKHPEVKSAI EGIKYIAETM KSDQESNNAA EEWK YVAMV MDHILLAVFM LVCIIGTLAV FAGRLIELNQ QG

UniProtKB: Acetylcholine receptor subunit alpha

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Macromolecule #2: Acetylcholine receptor subunit beta

MacromoleculeName: Acetylcholine receptor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 55.111832 KDa
SequenceString: SEAEGRLREK LFSGYDSTVR PAREVGDRVW VSIGLTLAQL ISLNEKDEEM STKVYLDLEW TDYRLSWDPE EHEGIDSLRI SAESVWLPD VVLLNNNDGN FDVALDINVV VSSDGSMRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ T GLSPEGQE ...String:
SEAEGRLREK LFSGYDSTVR PAREVGDRVW VSIGLTLAQL ISLNEKDEEM STKVYLDLEW TDYRLSWDPE EHEGIDSLRI SAESVWLPD VVLLNNNDGN FDVALDINVV VSSDGSMRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ T GLSPEGQE RQEVYIHEGT FIENGQWEII HKPSRLIQPS VDPRGGGEGR REEVTFYLII RRKPLFYLVN VIAPCILITL LA IFVFYLP PDAGEKMGLS IFALLTLTVF LLLLADKVPE TSLSVPIIIK YLMFTMVLVT FSVILSVVVL NLHHRSPHTH QMP LWVRQI FIHKLPLYLG LKRPKPERDQ MQEPPSIAPR DSPGSGWGRG TDEYFIRKPP NDFLFPKPNR FQPELSAPDL RRFI DGPNR AVGLPPELRE VVSSISYIAR QLQEQEDHDV LKEDWQFVAM VVDRLFLWTF IIFTSVGTLV IFLDATYHLP PADPF P

UniProtKB: Acetylcholine receptor subunit beta

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Macromolecule #3: Acetylcholine receptor subunit delta

MacromoleculeName: Acetylcholine receptor subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 56.543926 KDa
SequenceString: LNEEERLIRH LFEEKAYNKE LRPAAHKESV EISLALTLSN LISLKEVEET LTTNVWIEQG WTDSRLQWDA EDFGNISVLR LPADMVWLP EIVLENNNDG SFQISYSCNV LIYPSGSVYW LPPAIFRSSC PISVTYFPFD WQNCSLKFSS LKYTTKEITL S LKQAEEDG ...String:
LNEEERLIRH LFEEKAYNKE LRPAAHKESV EISLALTLSN LISLKEVEET LTTNVWIEQG WTDSRLQWDA EDFGNISVLR LPADMVWLP EIVLENNNDG SFQISYSCNV LIYPSGSVYW LPPAIFRSSC PISVTYFPFD WQNCSLKFSS LKYTTKEITL S LKQAEEDG RSYPVEWIII DPEGFTENGE WEIVHRPARV NVDPSVPLDS PNRQDVTFYL IIRRKPLFYV INILVPCVLI SF MINLVFY LPADCGEKTS MAISVLLAQS VFLLLISKRL PATSMAIPLI GKFLLFGMVL VTMVVVICVI VLNIHFRTPS THV LSEPVK KLFLETLPEI LHMSRPAEDG PSPGTLIRRS SSLGYISKAE EYFSLKSRSD LMFEKQSERH GLARRLTTAR RPPA GSEQA QQELFSELKP AVDGANFIVN HMKDQNNYNE EKDCWNRVAR TVDRLCLFVV TPIMVVGTAW IFLQGAYNQP PPQPF PGDP FSYLEKDKRF I

UniProtKB: Acetylcholine receptor subunit delta

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Macromolecule #4: Acetylcholine receptor subunit epsilon

MacromoleculeName: Acetylcholine receptor subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 52.613262 KDa
SequenceString: KNEELRLYHY LFDTYDPGRR PVQEPEDTVT ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSKG DFGGVETLRV PSELVWLPE IVLENNIDGQ FGVAYEANVL VSEGGYLSWL PPAIYRSTCA VEVTYFPFDW QNCSLVFRSQ TYNAEEVEFV F AVDDEGKT ...String:
KNEELRLYHY LFDTYDPGRR PVQEPEDTVT ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSKG DFGGVETLRV PSELVWLPE IVLENNIDGQ FGVAYEANVL VSEGGYLSWL PPAIYRSTCA VEVTYFPFDW QNCSLVFRSQ TYNAEEVEFV F AVDDEGKT ISKIDIDTEA YTENGEWAID FCPGVIRRHD GDSAGGPGET DVIYSLIIRR KPLFYVINII VPCVLISGLV LL AYFLPAQ AGGQKCTVSI NVLLAQTVFL FLIAQKTPET SLSVPLLGRY LIFVMVVATL IVMNCVIVLN VSLRTPTTHA MSP RLRYVL LELLPQLLGS GAPPEIPRAA SPPRRASSLG LLLRAEELIL KKPRSELVFE QQRHRHGTWT ATLCQNLGAA APEI RCCVD AVNFVASSTR DQEATGEEVS DWVRMGKALD SICFWAALVL FLVGSSLIFL GAYFNRVPQL PYPPCM

UniProtKB: Acetylcholine receptor subunit epsilon

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Macromolecule #5: Toxin

MacromoleculeName: Toxin / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.993089 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMICYNQQS SQPPTTKTCS ETSCYKKTWR DHRGTIIERG CGCPKVKPGI KLHCCRTDKC NN

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Macromolecule #10: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 10 / Number of copies: 8 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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 III (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: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 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: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209258
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: cryosparc ab initial model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9avv:
Bovine adult muscle nAChR resting state

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