[English] 日本語
Yorodumi
- EMDB-47017: Human muscle nAChR with fab9-bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47017
TitleHuman muscle nAChR with fab9-bound
Map data
Sample
  • Complex: Human muscle nicotinic acetylcholine receptor with MG fabs
    • 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: Fab9 heavy chain
    • Protein or peptide: Fab9 light chain
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshuman muscle / nicotinic acetylcholine receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


postsynaptic membrane organization / skeletal muscle tissue growth / musculoskeletal movement / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / behavioral response to nicotine / neuromuscular synaptic transmission ...postsynaptic membrane organization / skeletal muscle tissue growth / musculoskeletal movement / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / behavioral response to nicotine / neuromuscular synaptic transmission / acetylcholine-gated monoatomic cation-selective channel activity / muscle cell development / acetylcholine binding / synaptic transmission, cholinergic / monoatomic cation transmembrane transporter activity / nervous system process / acetylcholine receptor signaling pathway / ligand-gated monoatomic ion channel activity / postsynaptic specialization membrane / neuromuscular process / muscle cell cellular homeostasis / neuromuscular junction development / monoatomic cation transport / membrane depolarization / skeletal muscle contraction / neuronal action potential / muscle contraction / response to nicotine / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / neuromuscular junction / neuron cellular homeostasis / transmembrane signaling receptor activity / channel activity / monoatomic ion transmembrane transport / chemical synaptic transmission / 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 beta / Acetylcholine receptor subunit epsilon / Acetylcholine receptor subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.13 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: To Be Published
Title: Structure of human muscle AChR with fab9-bound
Authors: Li H / Hibbs RE
History
DepositionSep 14, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47017.png

Downloads & links

-
Map

FileDownload / File: emd_47017.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 400 pix.
= 374. Å		0.94 Å/pix.
x 400 pix.
= 374. Å		0.94 Å/pix.
x 400 pix.
= 374. 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: 0.095
Minimum - Maximum-0.76657677 - 1.445247
Average (Standard dev.)-0.00031633856 (±0.027034719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_47017_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47017_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Human muscle nicotinic acetylcholine receptor with MG fabs

EntireName: Human muscle nicotinic acetylcholine receptor with MG fabs
Components
  • Complex: Human muscle nicotinic acetylcholine receptor with MG fabs
    • 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: Fab9 heavy chain
    • Protein or peptide: Fab9 light chain
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: Human muscle nicotinic acetylcholine receptor with MG fabs

SupramoleculeName: Human muscle nicotinic acetylcholine receptor with MG fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

+
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: Homo sapiens (human)
Molecular weightTheoretical: 51.889266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL INVDEVNQIV TTNVRLKQQW VDYNLKWNP DDYGGVKKIH IPSEKIWRPD LVLYNNADGD FAIVKFTKVL LQYTGHITWT PPAIFKSYCE IIVTHFPFDE Q NCSMKLGT ...String:
MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL INVDEVNQIV TTNVRLKQQW VDYNLKWNP DDYGGVKKIH IPSEKIWRPD LVLYNNADGD FAIVKFTKVL LQYTGHITWT PPAIFKSYCE IIVTHFPFDE Q NCSMKLGT WTYDGSVVAI NPESDQPDLS NFMESGEWVI KESRGWKHSV TYSCCPDTPY LDITYHFVMQ RLPLYFIVNV II PCLLFSF LTGLVFYLPT DSGEKMTLSI SVLLSLTVFL LVIVELIPST SSAVPLIGKY MLFTMVFVIA SIIITVIVIN THH RSPSTH VMPNWVRKVF IDTIPNIMFF STMKRPSREK QDKKIFTEDI DISDISGKPG PPPMGFHSPL IKHPEVKSAI EGIK YIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ QG

UniProtKB: Acetylcholine receptor subunit alpha

+
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: Homo sapiens (human)
Molecular weightTheoretical: 56.843215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTPGALLMLL GALGAPLAPG VRGSEAEGRL REKLFSGYDS SVRPAREVGD RVRVSVGLIL AQLISLNEKD EEMSTKVYLD LEWTDYRLS WDPAEHDGID SLRITAESVW LPDVVLLNNN DGNFDVALDI SVVVSSDGSV RWQPPGIYRS SCSIQVTYFP F DWQNCTMV ...String:
MTPGALLMLL GALGAPLAPG VRGSEAEGRL REKLFSGYDS SVRPAREVGD RVRVSVGLIL AQLISLNEKD EEMSTKVYLD LEWTDYRLS WDPAEHDGID SLRITAESVW LPDVVLLNNN DGNFDVALDI SVVVSSDGSV RWQPPGIYRS SCSIQVTYFP F DWQNCTMV FSSYSYDSSE VSLQTGLGPD GQGHQEIHIH EGTFIENGQW EIIHKPSRLI QPPGDPRGGR EGQRQEVIFY LI IRRKPLF YLVNVIAPCI LITLLAIFVF YLPPDAGEKM GLSIFALLTL TVFLLLLADK VPETSLSVPI IIKYLMFTMV LVT FSVILS VVVLNLHHRS PHTHQMPLWV RQIFIHKLPL YLRLKRPKPE RDLMPEPPHC SSPGSGWGRG TDEYFIRKPP SDFL FPKPN RFQPELSAPD LRRFIDGPNR AVALLPELRE VVSSISYIAR QLQEQEDHDA LKEDWQFVAM VVDRLFLWTF IIFTS VGTL VIFLDATYHL PPPDPFPS

UniProtKB: Acetylcholine receptor subunit beta

+
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: Homo sapiens (human)
Molecular weightTheoretical: 58.955805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL SNLISLKEVE ETLTTNVWIE HGWTDNRLK WNAEEFGNIS VLRLPPDMVW LPEIVLENNN DGSFQISYSC NVLVYHYGFV YWLPPAIFRS SCPISVTYFP F DWQNCSLK ...String:
MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL SNLISLKEVE ETLTTNVWIE HGWTDNRLK WNAEEFGNIS VLRLPPDMVW LPEIVLENNN DGSFQISYSC NVLVYHYGFV YWLPPAIFRS SCPISVTYFP F DWQNCSLK FSSLKYTAKE ITLSLKQDAK ENRTYPVEWI IIDPEGFTEN GEWEIVHRPA RVNVDPRAPL DSPSRQDITF YL IIRRKPL FYIINILVPC VLISFMVNLV FYLPADSGEK TSVAISVLLA QSVFLLLISK RLPATSMAIP LIGKFLLFGM VLV TMVVVI CVIVLNIHFR TPSTHVLSEG VKKLFLETLP ELLHMSRPAE DGPSPGALVR RSSSLGYISK AEEYFLLKSR SDLM FEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPV MVVG TAWIFLQGVY NQPPPQPFPG DPYSYNVQDK RFI

UniProtKB: Acetylcholine receptor subunit delta

+
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: Homo sapiens (human)
Molecular weightTheoretical: 54.743754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSK DDFGGIETLR VPSELVWLPE IVLENNIDGQ FGVAYDANVL VYEGGSVTWL PPAIYRSVCA VEVTYFPFDW Q NCSLIFRS ...String:
MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSK DDFGGIETLR VPSELVWLPE IVLENNIDGQ FGVAYDANVL VYEGGSVTWL PPAIYRSVCA VEVTYFPFDW Q NCSLIFRS QTYNAEEVEF TFAVDNDGKT INKIDIDTEA YTENGEWAID FCPGVIRRHH GGATDGPGET DVIYSLIIRR KP LFYVINI IVPCVLISGL VLLAYFLPAQ AGGQKCTVSI NVLLAQTVFL FLIAQKIPET SLSVPLLGRF LIFVMVVATL IVM NCVIVL NVSQRTPTTH AMSPRLRHVL LELLPRLLGS PPPPEAPRAA SPPRRASSVG LLLRAEELIL KKPRSELVFE GQRH RQGTW TAAFCQSLGA AAPEVRCCVD AVNFVAESTR DQEATGEEVS DWVRMGNALD NICFWAALVL FSVGSSLIFL GAYFN RVPD LPYAPCIQP

UniProtKB: Acetylcholine receptor subunit epsilon

+
Macromolecule #5: Fab9 heavy chain

MacromoleculeName: Fab9 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.737609 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDSKGSSQKG SRLLLLLVVS NLLLCQGVVS AQVQLQESGP RLVKPSQTLS LTCTVSGGSV TRGNYYWTWI RQPAGKELEW IGHIYISGR TNFNPSLKSR VSISVDTSKN QFSLKLTSVT VADTAVYYCA REREVIVDRR RWLDPWGQGI LVTVSSASTK G PSVFPLAP ...String:
MDSKGSSQKG SRLLLLLVVS NLLLCQGVVS AQVQLQESGP RLVKPSQTLS LTCTVSGGSV TRGNYYWTWI RQPAGKELEW IGHIYISGR TNFNPSLKSR VSISVDTSKN QFSLKLTSVT VADTAVYYCA REREVIVDRR RWLDPWGQGI LVTVSSASTK G PSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NV NHKPSNT KVDKKVEPKS CGSHHHHHH

+
Macromolecule #6: Fab9 light chain

MacromoleculeName: Fab9 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.415482 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSD IVMTQSPSSL SASIGDRVTI TCRASHNISR YLSWFQQRPG KAPKLLIYAA SSLQSGVPSR FSGSGSGTD YTLTISNLHP EDFATYFCQQ SYSTPLIFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHSD IVMTQSPSSL SASIGDRVTI TCRASHNISR YLSWFQQRPG KAPKLLIYAA SSLQSGVPSR FSGSGSGTD YTLTISNLHP EDFATYFCQQ SYSTPLIFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

+
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: 4 / 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

+
Macromolecule #11: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 11 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

+
Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 397419
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more