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- EMDB-40239: Cryo-EM structure of Nav1.7 with CBZ -

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Basic information

Entry
Database: EMDB / ID: EMD-40239
TitleCryo-EM structure of Nav1.7 with CBZ
Map data
Sample
  • Complex: Human voltage-gated sodium channel Nav1.7 with beta subunits
    • Protein or peptide: Sodium channel protein type 9 subunit alpha
    • Protein or peptide: Sodium channel subunit beta-1
    • Protein or peptide: Sodium channel subunit beta-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: benzo[b][1]benzazepine-11-carboxamide
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
KeywordsCryo-EM / sodium channel / VGSC / Nav1.7 / MEMBRANE PROTEIN
Function / homology
Function and homology information


corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / response to pyrethroid / detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / membrane depolarization during Purkinje myocyte cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization ...corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / response to pyrethroid / detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / membrane depolarization during Purkinje myocyte cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / node of Ranvier / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity / locomotion / voltage-gated sodium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / sodium channel inhibitor activity / neuronal action potential propagation / Interaction between L1 and Ankyrins / sodium ion transport / behavioral response to pain / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / membrane depolarization / sodium ion transmembrane transport / sodium channel regulator activity / intercalated disc / sensory perception of pain / cardiac muscle contraction / T-tubule / post-embryonic development / axon guidance / positive regulation of neuron projection development / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to toxic substance / circadian rhythm / gene expression / nervous system development / response to heat / perikaryon / chemical synaptic transmission / transmembrane transporter binding / cell adhesion / inflammatory response / axon / synapse / extracellular region / plasma membrane
Similarity search - Function
Sodium channel subunit beta-1/beta-3 / Myelin P0 protein-related / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Sodium channel subunit beta-1/beta-3 / Myelin P0 protein-related / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ion transport domain / Ion transport protein / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sodium channel subunit beta-2 / Sodium channel subunit beta-1 / Sodium channel protein type 9 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFan X / Huang J / Yan N
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP) France
CitationJournal: Nat Commun / Year: 2023
Title: Structural mapping of Na1.7 antagonists.
Authors: Qiurong Wu / Jian Huang / Xiao Fan / Kan Wang / Xueqin Jin / Gaoxingyu Huang / Jiaao Li / Xiaojing Pan / Nieng Yan /
Abstract: Voltage-gated sodium (Na) channels are targeted by a number of widely used and investigational drugs for the treatment of epilepsy, arrhythmia, pain, and other disorders. Despite recent advances in ...Voltage-gated sodium (Na) channels are targeted by a number of widely used and investigational drugs for the treatment of epilepsy, arrhythmia, pain, and other disorders. Despite recent advances in structural elucidation of Na channels, the binding mode of most Na-targeting drugs remains unknown. Here we report high-resolution cryo-EM structures of human Na1.7 treated with drugs and lead compounds with representative chemical backbones at resolutions of 2.6-3.2 Å. A binding site beneath the intracellular gate (site BIG) accommodates carbamazepine, bupivacaine, and lacosamide. Unexpectedly, a second molecule of lacosamide plugs into the selectivity filter from the central cavity. Fenestrations are popular sites for various state-dependent drugs. We show that vinpocetine, a synthetic derivative of a vinca alkaloid, and hardwickiic acid, a natural product with antinociceptive effect, bind to the III-IV fenestration, while vixotrigine, an analgesic candidate, penetrates the IV-I fenestration of the pore domain. Our results permit building a 3D structural map for known drug-binding sites on Na channels summarized from the present and previous structures.
History
DepositionMar 27, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40239.png

Downloads & links

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Map

FileDownload / File: emd_40239.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.114 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-4.3983254 - 7.6876125
Average (Standard dev.)-0.0015375834 (±0.13020493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 356.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40239_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40239_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_40239_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human voltage-gated sodium channel Nav1.7 with beta subunits

EntireName: Human voltage-gated sodium channel Nav1.7 with beta subunits
Components
  • Complex: Human voltage-gated sodium channel Nav1.7 with beta subunits
    • Protein or peptide: Sodium channel protein type 9 subunit alpha
    • Protein or peptide: Sodium channel subunit beta-1
    • Protein or peptide: Sodium channel subunit beta-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: benzo[b][1]benzazepine-11-carboxamide
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: Human voltage-gated sodium channel Nav1.7 with beta subunits

SupramoleculeName: Human voltage-gated sodium channel Nav1.7 with beta subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium channel protein type 9 subunit alpha

MacromoleculeName: Sodium channel protein type 9 subunit alpha / type: protein_or_peptide / ID: 1 / Details: Carbamazepine / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 226.620047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAMLPPPGPQ SFVHFTKQSL ALIEQRIAER KSKEPKEEKK DDDEEAPKPS SDLEAGKQLP FIYGDIPPGM VSEPLEDLDP YYADKKTFI VLNKGKTIFR FNATPALYML SPFSPLRRIS IKILVHSLFS MLIMCTILTN CIFMTMNNPP DWTKNVEYTF T GIYTFESL ...String:
MAMLPPPGPQ SFVHFTKQSL ALIEQRIAER KSKEPKEEKK DDDEEAPKPS SDLEAGKQLP FIYGDIPPGM VSEPLEDLDP YYADKKTFI VLNKGKTIFR FNATPALYML SPFSPLRRIS IKILVHSLFS MLIMCTILTN CIFMTMNNPP DWTKNVEYTF T GIYTFESL VKILARGFCV GEFTFLRDPW NWLDFVVIVF AYLTEFVNLG NVSALRTFRV LRALKTISVI PGLKTIVGAL IQ SVKKLSD VMILTVFCLS VFALIGLQLF MGNLKHKCFR NSLENNETLE SIMNTLESEE DFRKYFYYLE GSKDALLCGF STD SGQCPE GYTCVKIGRN PDYGYTSFDT FSWAFLALFR LMTQDYWENL YQQTLRAAGK TYMIFFVVVI FLGSFYLINL ILAV VAMAY EEQNQANIEE AKQKELEFQQ MLDRLKKEQE EAEAIAAAAA EYTSIRRSRI MGLSESSSET SKLSSKSAKE RRNRR KKKN QKKLSSGEEK GDAEKLSKSE SEDSIRRKSF HLGVEGHRRA HEKRLSTPNQ SPLSIRGSLF SARRSSRTSL FSFKGR GRD IGSETEFADD EHSIFGDNES RRGSLFVPHR PQERRSSNIS QASRSPPMLP VNGKMHSAVD CNGVVSLVDG RSALMLP NG QLLPEVIIDK ATSDDSGTTN QIHKKRRCSS YLLSEDMLND PNLRQRAMSR ASILTNTVEE LEESRQKCPP WWYRFAHK F LIWNCSPYWI KFKKCIYFIV MDPFVDLAIT ICIVLNTLFM AMEHHPMTEE FKNVLAIGNL VFTGIFAAEM VLKLIAMDP YEYFQVGWNI FDSLIVTLSL VELFLADVEG LSVLRSFRLL RVFKLAKSWP TLNMLIKIIG NSVGALGNLT LVLAIIVFIF AVVGMQLFG KSYKECVCKI NDDCTLPRWH MNDFFHSFLI VFRVLCGEWI ETMWDCMEVA GQAMCLIVYM MVMVIGNLVV L NLFLALLL SSFSSDNLTA IEEDPDANNL QIAVTRIKKG INYVKQTLRE FILKAFSKKP KISREIRQAE DLNTKKENYI SN HTLAEMS KGHNFLKEKD KISGFGSSVD KHLMEDSDGQ SFIHNPSLTV TVPIAPGESD LENMNAEELS SDSDSEYSKV RLN RSSSSE CSTVDNPLPG EGEEAEAEPM NSDEPEACFT DGCVWRFSCC QVNIESGKGK IWWNIRKTCY KIVEHSWFES FIVL MILLS SGALAFEDIY IERKKTIKII LEYADKIFTY IFILEMLLKW IAYGYKTYFT NAWCWLDFLI VDVSLVTLVA NTLGY SDLG PIKSLRTLRA LRPLRALSRF EGMRVVVNAL IGAIPSIMNV LLVCLIFWLI FSIMGVNLFA GKFYECINTT DGSRFP ASQ VPNRSECFAL MNVSQNVRWK NLKVNFDNVG LGYLSLLQVA TFKGWTIIMY AAVDSVNVDK QPKYEYSLYM YIYFVVF II FGSFFTLNLF IGVIIDNFNQ QKKKLGGQDI FMTEEQKKYY NAMKKLGSKK PQKPIPRPGN KIQGCIFDLV TNQAFDIS I MVLICLNMVT MMVEKEGQSQ HMTEVLYWIN VVFIILFTGE CVLKLISLRH YYFTVGWNIF DFVVVIISIV GMFLADLIE TYFVSPTLFR VIRLARIGRI LRLVKGAKGI RTLLFALMMS LPALFNIGLL LFLVMFIYAI FGMSNFAYVK KEDGINDMFN FETFGNSMI CLFQITTSAG WDGLLAPILN SKPPDCDPKK VHPGSSVEGD CGNPSVGIFY FVSYIIISFL VVVNMYIAVI L ENFSVATE ESTEPLSEDD FEMFYEVWEK FDPDATQFIE FSKLSDFAAA LDPPLLIAKP NKVQLIAMDL PMVSGDRIHC LD ILFAFTK RVLGESGEMD SLRSQMEERF MSANPSKVSY EPITTTLKRK QEDVSATVIQ RAYRRYRLRQ NVKNISSIYI KDG DRDDDL LNKKDMAFDN VNENSSPEKT DATSSTTSPP SYDSVTKPDK EKYEQDRTEK EDKGKDSKES KK

UniProtKB: Sodium channel protein type 9 subunit alpha

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Macromolecule #2: Sodium channel subunit beta-1

MacromoleculeName: Sodium channel subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.732115 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRLLALVVG AALVSSACGG CVEVDSETEA VYGMTFKILC ISCKRRSETN AETFTEWTFR QKGTEEFVKI LRYENEVLQL EEDERFEGR VVWNGSRGTK DLQDLSIFIT NVTYNHSGDY ECHVYRLLFF ENYEHNTSVV KKIHIEVVDK ANRDMASIVS E IMMYVLIV ...String:
MGRLLALVVG AALVSSACGG CVEVDSETEA VYGMTFKILC ISCKRRSETN AETFTEWTFR QKGTEEFVKI LRYENEVLQL EEDERFEGR VVWNGSRGTK DLQDLSIFIT NVTYNHSGDY ECHVYRLLFF ENYEHNTSVV KKIHIEVVDK ANRDMASIVS E IMMYVLIV VLTIWLVAEM IYCYKKIAAA TETAAQENAS EYLAITSESK ENCTGVQVAE

UniProtKB: Sodium channel subunit beta-1

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Macromolecule #3: Sodium channel subunit beta-2

MacromoleculeName: Sodium channel subunit beta-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.355859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHRDAWLPRP AFSLTGLSLF FSLVPPGRSM EVTVPATLNV LNGSDARLPC TFNSCYTVNH KQFSLNWTYQ ECNNCSEEMF LQFRMKIIN LKLERFQDRV EFSGNPSKYD VSVMLRNVQP EDEGIYNCYI MNPPDRHRGH GKIHLQVLME EPPERDSTVA V IVGASVGG ...String:
MHRDAWLPRP AFSLTGLSLF FSLVPPGRSM EVTVPATLNV LNGSDARLPC TFNSCYTVNH KQFSLNWTYQ ECNNCSEEMF LQFRMKIIN LKLERFQDRV EFSGNPSKYD VSVMLRNVQP EDEGIYNCYI MNPPDRHRGH GKIHLQVLME EPPERDSTVA V IVGASVGG FLAVVILVLM VVKCVRRKKE QKLSTDDLKT EEEGKTDGEG NPDDGAK

UniProtKB: Sodium channel subunit beta-2

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #6: benzo[b][1]benzazepine-11-carboxamide

MacromoleculeName: benzo[b][1]benzazepine-11-carboxamide / type: ligand / ID: 6 / Number of copies: 1 / Formula: N6W
Molecular weightTheoretical: 236.269 Da
Chemical component information

ChemComp-N6W:
benzo[b][1]benzazepine-11-carboxamide / medication*YM / Carbamazepine

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Macromolecule #7: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 7 / Number of copies: 3 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / Phosphatidylserine

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Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 5 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #9: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / Number of copies: 9 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

ChemComp-LPE:
1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Macromolecule #10: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 10 / Number of copies: 4 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287917
FSC plot (resolution estimation)

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