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- EMDB-51571: Human adult muscle nAChR in desensitised state in nanodisc with 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-51571
TitleHuman adult muscle nAChR in desensitised state in nanodisc with 1 mM acetylcholine
Map dataCryoSPARC map used for final model refinement, sharpend with a b-factor of -20
Sample
  • Complex: Human adult muscle nAChR in desensitised state in nanodisc with 1 mM acetylcholine
    • 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,Green fluorescent protein
    • Protein or peptide: Fab35 light chain
    • Protein or peptide: Fab35 heavy chain
  • Ligand: ACETYLCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLigand-gated ion channel / nicotinic receptor / pLGIC / cys-loop 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 / neuromuscular synaptic transmission / behavioral response to nicotine ...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 / neuromuscular synaptic transmission / behavioral response to nicotine / acetylcholine-gated monoatomic cation-selective channel activity / muscle cell development / acetylcholine binding / nervous system process / synaptic transmission, cholinergic / monoatomic cation transmembrane transporter activity / acetylcholine receptor signaling pathway / ligand-gated monoatomic ion channel activity / muscle cell cellular homeostasis / neuromuscular process / postsynaptic specialization membrane / neuromuscular junction development / monoatomic cation transport / membrane depolarization / skeletal muscle contraction / neuronal action potential / muscle contraction / bioluminescence / regulation of membrane potential / generation of precursor metabolites and energy / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nicotine / 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 / Green fluorescent protein, GFP / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain ...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 / Green fluorescent protein, GFP / 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 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Acetylcholine receptor subunit beta / Green fluorescent protein / Acetylcholine receptor subunit epsilon / Acetylcholine receptor subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLi A / Pike ACW / Chi G / Webster R / Maxwell S / Liu W / Beeson D / Sauer DB / Dong YY
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust102161/Z/13/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/Y012623/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 18, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51571.png

Downloads & links

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Map

FileDownload / File: emd_51571.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC map used for final model refinement, sharpend with a b-factor of -20
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 360 pix.
= 421.2 Å		1.17 Å/pix.
x 360 pix.
= 421.2 Å		1.17 Å/pix.
x 360 pix.
= 421.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.2047819 - 2.3987017
Average (Standard dev.)-0.00013018081 (±0.032380406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 421.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51571_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_51571_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map from cryoSPARC non-uniform refinement

Fileemd_51571_additional_1.map
Annotationunsharpened map from cryoSPARC non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B from cryoSPARC non-uniform refinement

Fileemd_51571_half_map_1.map
Annotationhalf map B from cryoSPARC non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A from cryoSPARC non-uniform refinement

Fileemd_51571_half_map_2.map
Annotationhalf map A from cryoSPARC non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human adult muscle nAChR in desensitised state in nanodisc with 1...

EntireName: Human adult muscle nAChR in desensitised state in nanodisc with 1 mM acetylcholine
Components
  • Complex: Human adult muscle nAChR in desensitised state in nanodisc with 1 mM acetylcholine
    • 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,Green fluorescent protein
    • Protein or peptide: Fab35 light chain
    • Protein or peptide: Fab35 heavy chain
  • Ligand: ACETYLCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human adult muscle nAChR in desensitised state in nanodisc with 1...

SupramoleculeName: Human adult muscle nAChR in desensitised state in nanodisc with 1 mM acetylcholine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: nAChR in complex with acetylcholine and Fab35 in MSP2N2-soy polar lipids nanodiscs
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 386 KDa

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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: Homo sapiens (human)
Molecular weightTheoretical: 49.747645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPD LVLYNNADGD FAIVKFTKVL LQYTGHITWT PPAIFKSYCE IIVTHFPFDE QNCSMKLGTW TYDGSVVAIN P ESDQPDLS ...String:
SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPD LVLYNNADGD FAIVKFTKVL LQYTGHITWT PPAIFKSYCE IIVTHFPFDE QNCSMKLGTW TYDGSVVAIN P ESDQPDLS NFMESGEWVI KESRGWKHSV TYSCCPDTPY LDITYHFVMQ RLPLYFIVNV IIPCLLFSFL TGLVFYLPTD SG EKMTLSI SVLLSLTVFL LVIVELIPST SSAVPLIGKY MLFTMVFVIA SIIITVIVIN THHRSPSTHV MPNWVRKVFI DTI PNIMFF STMKRPSREK QDKKIFTEDI DISDISGKPG PPPMGFHSPL IKHPEVKSAI EGIKYIAETM KSDQESNNAA AEWK YVAMV MDHILLGVFM 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: Homo sapiens (human)
Molecular weightTheoretical: 54.596477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SEAEGRLREK LFSGYDSSVR PAREVGDRVR VSVGLILAQL ISLNEKDEEM STKVYLDLEW TDYRLSWDPA EHDGIDSLRI TAESVWLPD VVLLNNNDGN FDVALDISVV VSSDGSVRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ T GLGPDGQG ...String:
SEAEGRLREK LFSGYDSSVR PAREVGDRVR VSVGLILAQL ISLNEKDEEM STKVYLDLEW TDYRLSWDPA EHDGIDSLRI TAESVWLPD VVLLNNNDGN FDVALDISVV VSSDGSVRWQ PPGIYRSSCS IQVTYFPFDW QNCTMVFSSY SYDSSEVSLQ T GLGPDGQG HQEIHIHEGT FIENGQWEII HKPSRLIQPP GDPRGGREGQ RQEVIFYLII RRKPLFYLVN VIAPCILITL LA IFVFYLP PDAGEKMGLS IFALLTLTVF LLLLADKVPE TSLSVPIIIK YLMFTMVLVT FSVILSVVVL NLHHRSPHTH QMP LWVRQI FIHKLPLYLR LKRPKPERDL MPEPPHCSSP GSGWGRGTDE YFIRKPPSDF LFPKPNRFQP ELSAPDLRRF IDGP NRAVA LLPELREVVS SISYIARQLQ EQEDHDALKE DWQFVAMVVD RLFLWTFIIF TSVGTLVIFL DATYHLPPPD PFP

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: Homo sapiens (human)
Molecular weightTheoretical: 56.915359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LNEEERLIRH LFQEKGYNKE LRPVAHKEES VDVALALTLS NLISLKEVEE TLTTNVWIEH GWTDNRLKWN AEEFGNISVL RLPPDMVWL PEIVLENNND GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFS SLKYTAKEIT L SLKQDAKE ...String:
LNEEERLIRH LFQEKGYNKE LRPVAHKEES VDVALALTLS NLISLKEVEE TLTTNVWIEH GWTDNRLKWN AEEFGNISVL RLPPDMVWL PEIVLENNND GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFS SLKYTAKEIT L SLKQDAKE NRTYPVEWII IDPEGFTENG EWEIVHRPAR VNVDPRAPLD SPSRQDITFY LIIRRKPLFY IINILVPCVL IS FMVNLVF YLPADSGEKT SVAISVLLAQ SVFLLLISKR LPATSMAIPL IGKFLLFGMV LVTMVVVICV IVLNIHFRTP STH VLSEGV KKLFLETLPE LLHMSRPAED GPSPGALVRR SSSLGYISKA EEYFLLKSRS DLMFEKQSER HGLARRLTTA RRPP ASSEQ AQQELFNELK PAVDGANFIV NHMRDQNNYN EEKDSWNRVA RTVDRLCLFV VTPVMVVGTA WIFLQGVYNQ PPPQP FPGD PYSYNVQDKR FI

UniProtKB: Acetylcholine receptor subunit delta

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Macromolecule #4: Acetylcholine receptor subunit epsilon,Green fluorescent protein

MacromoleculeName: Acetylcholine receptor subunit epsilon,Green fluorescent protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.60375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV PSELVWLPE IVLENNIDGQ FGVAYDANVL VYEGGSVTWL PPAIYRSVCA VEVTYFPFDW QNCSLIFRSQ TYNAEEVEFT F AVDNDGKT ...String:
KNEELRLYHH LFNNYDPGSR PVREPEDTVT ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV PSELVWLPE IVLENNIDGQ FGVAYDANVL VYEGGSVTWL PPAIYRSVCA VEVTYFPFDW QNCSLIFRSQ TYNAEEVEFT F AVDNDGKT INKIDIDTEA YTENGEWAID FCPGVIRRHH GGATDGPGET DVIYSLIIRR KPLFYVINII VPCVLISGLV LL AYFLPAQ AGGQKCTVSI NVLLAQTVFL FLIAQKIPET SLSVPLLGRF LIFVMVVATL IVMNCVIVLN VSQRTPTTHA MSP RLRHVL LELLPRLLGS PPPPEAPRAP PVATMVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK FICT TGKLP VPWPTLVTTL TYGVQCFSRY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYKTRAEVKF EGDTLVNRIE LKGID FKED GNILGHKLEY NYNSHNVYIM ADKQKNGIKV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDNHYLST QSALSK DPN EKRDHMVLLE FVTAAGITLG MDELYKAPRA ASPPRRASSV GLLLRAEELI LKKPRSELVF EGQRHRQGTW TAAFCQS LG AAAPEVRCCV DAVNFVAEST RDQEATGEEV SDWVRMGNAL DNICFWAALV LFSVGSSLIF LGAYFNRVPD LPYAPCIQ P

UniProtKB: Acetylcholine receptor subunit epsilon, Green fluorescent protein, Acetylcholine receptor subunit epsilon

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Macromolecule #5: Fab35 light chain

MacromoleculeName: Fab35 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 23.392982 KDa
Recombinant expressionOrganism: Rattus norvegicus (Norway rat)
SequenceString: DIVITQSPSL LSASVGDRVT LTCKGSQNID NYLAWYQQKL GEAPKLLIYK TNSLQTGIPS RFSGSGSGTD YTLTISSLHS EDLATYYCY QYINGYTFGT GTKLELKRAD AAPTVSIFPP STEQLATGGA SVVCLMNNFY PRDISVKWKI DGTERRDGVL D SVTDQDSK ...String:
DIVITQSPSL LSASVGDRVT LTCKGSQNID NYLAWYQQKL GEAPKLLIYK TNSLQTGIPS RFSGSGSGTD YTLTISSLHS EDLATYYCY QYINGYTFGT GTKLELKRAD AAPTVSIFPP STEQLATGGA SVVCLMNNFY PRDISVKWKI DGTERRDGVL D SVTDQDSK DSTYSMSSTL SLTKADYESH NLYTCEVVHK TSSSPVVKSF NRNEC

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Macromolecule #6: Fab35 heavy chain

MacromoleculeName: Fab35 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 23.879758 KDa
Recombinant expressionOrganism: Rattus norvegicus (Norway rat)
SequenceString: EVQLQESGPG LVQPSETLSL TCTVSGFSLT SYSVSWLRQP SGKGPEWMGR MWDDGGTVYN SGLKSRLSIS RDTSKNQVFL KMNSLQTDD TGTYYCTRDE RIRAINWFAY WGQGTLVTVS SAETTAPSVY PLAPGTALKS NSMVTLGCLV KGYFPEPVTV T WNSGALSS ...String:
EVQLQESGPG LVQPSETLSL TCTVSGFSLT SYSVSWLRQP SGKGPEWMGR MWDDGGTVYN SGLKSRLSIS RDTSKNQVFL KMNSLQTDD TGTYYCTRDE RIRAINWFAY WGQGTLVTVS SAETTAPSVY PLAPGTALKS NSMVTLGCLV KGYFPEPVTV T WNSGALSS GVHTFPAVLQ SGLYTLTSSV TVPSSTWPSQ TVTCNVAHPG QQHQRWTRKL C

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Macromolecule #11: ACETYLCHOLINE

MacromoleculeName: ACETYLCHOLINE / type: ligand / ID: 11 / Number of copies: 2 / Formula: ACH
Molecular weightTheoretical: 146.207 Da
Chemical component information

ChemComp-ACH:
ACETYLCHOLINE / neurotransmitter*YM

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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

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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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride

Details: 20 mM HEPES pH 7.5, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.35 K / Instrument: FEI VITROBOT MARK IV / Details: 2.5 ul sample, blot time=4 s, blot force=-10.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 19925 / Average exposure time: 1.7 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5168840 / Details: extracted by topaz picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio model from cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Details: non-uniform refinenement / Number images used: 434976
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 65560 / Software - Name: RELION (ver. 5.0.0)
Details: Class3D without alignment (10 classes, t=20) with a mask covering the extracellular domain of nAChR
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2708

source_name: AlphaFold, initial_model_type: in silico model

1230

source_name: AlphaFold, initial_model_type: in silico model

7001

source_name: AlphaFold, initial_model_type: in silico model

4844

source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.6.1)
DetailsInitial fitting of alphafold models using chimeraX followed by manual rebuilding in COOT and final refinement in ISOLDE and PHENIX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9gu3:
Human adult muscle nAChR in desensitised state in nanodisc with 1 mM acetylcholine

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