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- EMDB-40754: The 3alpha2beta stoichiometry of human alpha4beta2 nicotinic acet... -

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Basic information

Entry
Database: EMDB / ID: EMD-40754
TitleThe 3alpha2beta stoichiometry of human alpha4beta2 nicotinic acetylcholine receptor in complex with acetylcholine and calcium
Map data
Sample
  • Complex: A complex of two Fab fragments with the 3alpha2beta stoichiometry of human alpha4beta2 nicotinic receptor bound to acetylcholine and calcium
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-4
    • Protein or peptide: Neuronal acetylcholine receptor subunit beta-2
    • Protein or peptide: IgG1 Kappa Light Chain
    • Protein or peptide: IgG1 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ACETYLCHOLINE
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
  • Ligand: water
Keywordscys-loop ligand-gated pentameric ion channels / cation-selective channel / acetylcholine / calcium / TRANSPORT PROTEIN
Function / homology
Function and homology information


vestibulocochlear nerve development / lateral geniculate nucleus development / regulation of circadian sleep/wake cycle, REM sleep / regulation of synaptic transmission, dopaminergic / quaternary ammonium group binding / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / optic nerve morphogenesis / response to acetylcholine ...vestibulocochlear nerve development / lateral geniculate nucleus development / regulation of circadian sleep/wake cycle, REM sleep / regulation of synaptic transmission, dopaminergic / quaternary ammonium group binding / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / optic nerve morphogenesis / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / central nervous system projection neuron axonogenesis / acetylcholine-gated channel complex / regulation of dopamine metabolic process / cholinergic synapse / negative regulation of action potential / behavioral response to nicotine / positive regulation of dopamine secretion / acetylcholine receptor activity / inhibitory postsynaptic potential / synaptic transmission, cholinergic / acetylcholine binding / postsynaptic specialization membrane / nervous system process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / regulation of synapse assembly / action potential / regulation of dendrite morphogenesis / heterocyclic compound binding / regulation of dopamine secretion / B cell activation / plasma membrane raft / associative learning / membrane depolarization / social behavior / ligand-gated monoatomic ion channel activity / smooth muscle contraction / monoatomic ion transport / positive regulation of B cell proliferation / sensory perception of pain / visual perception / response to cocaine / learning / locomotory behavior / regulation of membrane potential / sensory perception of sound / response to nicotine / visual learning / memory / cognition / calcium ion transport / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / response to ethanol / response to oxidative stress / response to hypoxia / neuron projection / external side of plasma membrane / DNA repair / neuronal cell body / synapse / dendrite / protein-containing complex binding / signal transduction / membrane / 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
Neuronal acetylcholine receptor subunit beta-2 / Neuronal acetylcholine receptor subunit alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsKang G / Hibbs RE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA047848 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA042072 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS120496 United States
CitationJournal: To Be Published
Title: Structure of the 3alpha2beta stoichiometry of the human alpha4beta2 nicotinic acetylcholine receptor in complex with acetylcholine and calcium
Authors: Kang G / Mazzaferro S / Natarajan K / Sine S / Hibbs RE
History
DepositionMay 9, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40754.png

Downloads & links

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Map

FileDownload / File: emd_40754.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0694 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09625575 - 0.21966517
Average (Standard dev.)0.0006067583 (±0.005626333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 320.81998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40754_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40754_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 : A complex of two Fab fragments with the 3alpha2beta stoichiometry...

EntireName: A complex of two Fab fragments with the 3alpha2beta stoichiometry of human alpha4beta2 nicotinic receptor bound to acetylcholine and calcium
Components
  • Complex: A complex of two Fab fragments with the 3alpha2beta stoichiometry of human alpha4beta2 nicotinic receptor bound to acetylcholine and calcium
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-4
    • Protein or peptide: Neuronal acetylcholine receptor subunit beta-2
    • Protein or peptide: IgG1 Kappa Light Chain
    • Protein or peptide: IgG1 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ACETYLCHOLINE
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: A complex of two Fab fragments with the 3alpha2beta stoichiometry...

SupramoleculeName: A complex of two Fab fragments with the 3alpha2beta stoichiometry of human alpha4beta2 nicotinic receptor bound to acetylcholine and calcium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuronal acetylcholine receptor subunit alpha-4

MacromoleculeName: Neuronal acetylcholine receptor subunit alpha-4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.862367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSHVETRAHA EERLLKKLFS GYNKWSRPVA NISDVVLVRF GLSIAQLIDV DEKNQMMTTN VWVKQEWHDY KLRWDPADYE NVTSIRIPS ELIWRPDIVL YNNADGDFAV THLTKAHLFH DGRVQWTPPA IYKSSCSIDV TFFPFDQQNC TMKFGSWTYD K AKIDLVNM ...String:
SSHVETRAHA EERLLKKLFS GYNKWSRPVA NISDVVLVRF GLSIAQLIDV DEKNQMMTTN VWVKQEWHDY KLRWDPADYE NVTSIRIPS ELIWRPDIVL YNNADGDFAV THLTKAHLFH DGRVQWTPPA IYKSSCSIDV TFFPFDQQNC TMKFGSWTYD K AKIDLVNM HSRVDQLDFW ESGEWVIVDA VGTYNTRKYE CCAEIYPDIT YAFVIRRLPL FYTINLIIPC LLISCLTVLV FY LPSECGE KITLCISVLL SLTVFLLLIT EIIPSTSLVI PLIGEYLLFT MIFVTLSIVI TVFVLNVHHR SPRTHTMPTW VRR VFLDIV PRLLLMKRPS VVDTDFERSV KEDWKYVAMV IDRIFLWMFI IVCLLGTVGL FLPPWLAGMI

UniProtKB: Neuronal acetylcholine receptor subunit alpha-4, Neuronal acetylcholine receptor subunit alpha-4

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Macromolecule #2: Neuronal acetylcholine receptor subunit beta-2

MacromoleculeName: Neuronal acetylcholine receptor subunit beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.748863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TDTEERLVEH LLDPSRYNKL IRPATNGSEL VTVQLMVSLA QLISVHEREQ IMTTNVWLTQ EWEDYRLTWK PEEFDNMKKV RLPSKHIWL PDVVLYNNAD GMYEVSFYSN AVVSYDGSIF WLPPAIYKSA CKIEVKHFPF DQQNCTMKFR SWTYDRTEID L VLKSEVAS ...String:
TDTEERLVEH LLDPSRYNKL IRPATNGSEL VTVQLMVSLA QLISVHEREQ IMTTNVWLTQ EWEDYRLTWK PEEFDNMKKV RLPSKHIWL PDVVLYNNAD GMYEVSFYSN AVVSYDGSIF WLPPAIYKSA CKIEVKHFPF DQQNCTMKFR SWTYDRTEID L VLKSEVAS LDDFTPSGEW DIVALPGRRN ENPDDSTYVD ITYDFIIRRK PLFYTINLII PCVLITSLAI LVFYLPSDCG EK MTLCISV LLALTVFLLL ISKIVPPTSL DVPLVGKYLM FTMVLVTFSI VTSVCVLNVH HRSPTTHTMA PWVKVVFLEK LPA LLFMQQ PRHHDDDQER SVSEDWKYVA MVIDRLFLWI FVFVCVFGTI GMFLQPLFQN YTTTTFLHSD HSAPSSKSAW SHPQ FEK

UniProtKB: Neuronal acetylcholine receptor subunit beta-2, Neuronal acetylcholine receptor subunit beta-2

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Macromolecule #3: IgG1 Kappa Light Chain

MacromoleculeName: IgG1 Kappa Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.378596 KDa
SequenceString: MKLPVRLLVL MFWIPASSSD VLMTQTPLSL PVSLGDQASI SCRSSQSIVH SNGNTYLEWY LQKPGQSPKL LIYKVSNRFS GVPDRFSGS GSGTDFTLKI SRVEAEDLGV YYCFQGSHVP WTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI ...String:
MKLPVRLLVL MFWIPASSSD VLMTQTPLSL PVSLGDQASI SCRSSQSIVH SNGNTYLEWY LQKPGQSPKL LIYKVSNRFS GVPDRFSGS GSGTDFTLKI SRVEAEDLGV YYCFQGSHVP WTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF L NNFYPKDI NVKWKIDGSE RQNGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #4: IgG1 Heavy Chain

MacromoleculeName: IgG1 Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.195668 KDa
SequenceString: MEWTWVFLFL LSVTAGVHSQ VQLQQSGAEV MKPGASVKIS CKGTGYTFSS YWIEWVKQRP GHGLERIGEI LPGSGSTNYN EKFRGKATF TADKSSKTAY MQLSSLTSED SAVYYCARYL PYYYAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS M VTLGCLVK ...String:
MEWTWVFLFL LSVTAGVHSQ VQLQQSGAEV MKPGASVKIS CKGTGYTFSS YWIEWVKQRP GHGLERIGEI LPGSGSTNYN EKFRGKATF TADKSSKTAY MQLSSLTSED SAVYYCARYL PYYYAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS M VTLGCLVK GYFPEPVTVT WNSGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR DC GCKPCIC TVPEVSSVFI FPPKPKDVLT ITLTPKVTCV VVDISKDDPE VQFSWFVDDV EVHTAQTQPR EEQFNSTFRS VSE LPIMHQ DWLNGKEFKC RVNSAAFPAP IEKTISKTKG RPKAPQVYTI PPPKEQMAKD KVSLTCMITD FFPEDITVEW QWNG QPAEN YKNTQPIMDT DGSYFVYSKL NVQKSNWEAG NTFTCSVLHE GLHNHHTEKS LSHSPGK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: ACETYLCHOLINE

MacromoleculeName: ACETYLCHOLINE / type: ligand / ID: 7 / Number of copies: 3 / Formula: ACH
Molecular weightTheoretical: 146.207 Da
Chemical component information

ChemComp-ACH:
ACETYLCHOLINE / neurotransmitter*YM

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 9 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #10: water

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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6cnk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51470
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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