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- EMDB-35975: Structure of human Nav1.7 in complex with Hardwickii acid -

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Entry
Database: EMDB / ID: EMD-35975
TitleStructure of human Nav1.7 in complex with Hardwickii acid
Map data
Sample
  • Complex: human Nav1.7 in complex with hardwickii acid
    • Protein or peptide: Sodium channel subunit beta-1
  • Protein or peptide: Sodium channel protein type 9 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsInhibitor complex. / MEMBRANE PROTEIN
Function / homology
Function and homology information


corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / action potential propagation / detection of mechanical stimulus involved in sensory perception / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport ...corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / action potential propagation / detection of mechanical stimulus involved in sensory perception / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport / regulation of sodium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / cardiac muscle cell action potential involved in contraction / node of Ranvier / voltage-gated sodium channel complex / sodium channel inhibitor activity / locomotion / neuronal action potential propagation / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / detection of temperature stimulus involved in sensory perception of pain / Phase 0 - rapid depolarisation / behavioral response to pain / regulation of heart rate by cardiac conduction / intercalated disc / sodium channel regulator activity / membrane depolarization / neuronal action potential / cardiac muscle contraction / axon terminus / sensory perception of pain / T-tubule / sodium ion transmembrane transport / axon guidance / post-embryonic development / positive regulation of neuron projection development / circadian rhythm / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / perikaryon / transmembrane transporter binding / cell adhesion / inflammatory response / axon / extracellular region / plasma membrane
Similarity search - Function
Sodium channel subunit beta-1/beta-3 / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / 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 / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / 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-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sodium channel regulatory subunit beta-1 / Sodium channel protein type 9 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWu QR / Yan N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271252 China
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
DepositionApr 19, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35975.png

Downloads & links

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Map

FileDownload / File: emd_35975.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-2.1853251 - 3.6765664
Average (Standard dev.)0.008615271 (±0.09392819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35975_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35975_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : human Nav1.7 in complex with hardwickii acid

EntireName: human Nav1.7 in complex with hardwickii acid
Components
  • Complex: human Nav1.7 in complex with hardwickii acid
    • Protein or peptide: Sodium channel subunit beta-1
  • Protein or peptide: Sodium channel protein type 9 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: human Nav1.7 in complex with hardwickii acid

SupramoleculeName: human Nav1.7 in complex with hardwickii acid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230.9225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WSHPQFEKGG GARGGSGGGS WSHPQFEKGF DYKDDDDKGT MAMLPPPGPQ SFVHFTKQSL ALIEQRIAER KSKEPKEEKK DDDEEAPKP SSDLEAGKQL PFIYGDIPPG MVSEPLEDLD PYYADKKTFI VLNKGKTIFR FNATPALYML SPFSPLRRIS I KILVHSLF ...String:
WSHPQFEKGG GARGGSGGGS WSHPQFEKGF DYKDDDDKGT MAMLPPPGPQ SFVHFTKQSL ALIEQRIAER KSKEPKEEKK DDDEEAPKP SSDLEAGKQL PFIYGDIPPG MVSEPLEDLD PYYADKKTFI VLNKGKTIFR FNATPALYML SPFSPLRRIS I KILVHSLF SMLIMCTILT NCIFMTMNNP PDWTKNVEYT FTGIYTFESL VKILARGFCV GEFTFLRDPW NWLDFVVIVF AY LTEFVNL GNVSALRTFR VLRALKTISV IPGLKTIVGA LIQSVKKLSD VMILTVFCLS VFALIGLQLF MGNLKHKCFR NSL ENNETL ESIMNTLESE EDFRKYFYYL EGSKDALLCG FSTDSGQCPE GYTCVKIGRN PDYGYTSFDT FSWAFLALFR LMTQ DYWEN LYQQTLRAAG KTYMIFFVVV IFLGSFYLIN LILAVVAMAY EEQNQANIEE AKQKELEFQQ MLDRLKKEQE EAEAI AAAA AEYTSIRRSR IMGLSESSSE TSKLSSKSAK ERRNRRKKKN QKKLSSGEEK GDAEKLSKSE SEDSIRRKSF HLGVEG HRR AHEKRLSTPN QSPLSIRGSL FSARRSSRTS LFSFKGRGRD IGSETEFADD EHSIFGDNES RRGSLFVPHR PQERRSS NI SQASRSPPML PVNGKMHSAV DCNGVVSLVD GRSALMLPNG QLLPEVIIDK ATSDDSGTTN QIHKKRRCSS YLLSEDML N DPNLRQRAMS RASILTNTVE ELEESRQKCP PWWYRFAHKF LIWNCSPYWI KFKKCIYFIV MDPFVDLAIT ICIVLNTLF MAMEHHPMTE EFKNVLAIGN LVFTGIFAAE MVLKLIAMDP YEYFQVGWNI FDSLIVTLSL VELFLADVEG LSVLRSFRLL RVFKLAKSW PTLNMLIKII GNSVGALGNL TLVLAIIVFI FAVVGMQLFG KSYKECVCKI NDDCTLPRWH MNDFFHSFLI V FRVLCGEW IETMWDCMEV AGQAMCLIVY MMVMVIGNLV VLNLFLALLL SSFSSDNLTA IEEDPDANNL QIAVTRIKKG IN YVKQTLR EFILKAFSKK PKISREIRQA EDLNTKKENY ISNHTLAEMS KGHNFLKEKD KISGFGSSVD KHLMEDSDGQ SFI HNPSLT VTVPIAPGES DLENMNAEEL SSDSDSEYSK VRLNRSSSSE CSTVDNPLPG EGEEAEAEPM NSDEPEACFT DGCV WRFSC CQVNIESGKG KIWWNIRKTC YKIVEHSWFE SFIVLMILLS SGALAFEDIY IERKKTIKII LEYADKIFTY IFILE MLLK WIAYGYKTYF TNAWCWLDFL IVDVSLVTLV ANTLGYSDLG PIKSLRTLRA LRPLRALSRF EGMRVVVNAL IGAIPS IMN VLLVCLIFWL IFSIMGVNLF AGKFYECINT TDGSRFPASQ VPNRSECFAL MNVSQNVRWK NLKVNFDNVG LGYLSLL QV ATFKGWTIIM YAAVDSVNVD KQPKYEYSLY MYIYFVVFII FGSFFTLNLF IGVIIDNFNQ QKKKLGGQDI FMTEEQKK Y YNAMKKLGSK KPQKPIPRPG NKIQGCIFDL VTNQAFDISI MVLICLNMVT MMVEKEGQSQ HMTEVLYWIN VVFIILFTG ECVLKLISLR HYYFTVGWNI FDFVVVIISI VGMFLADLIE TYFVSPTLFR VIRLARIGRI LRLVKGAKGI RTLLFALMMS LPALFNIGL LLFLVMFIYA IFGMSNFAYV KKEDGINDMF NFETFGNSMI CLFQITTSAG WDGLLAPILN SKPPDCDPKK V HPGSSVEG DCGNPSVGIF YFVSYIIISF LVVVNMYIAV ILENFSVATE ESTEPLSEDD FEMFYEVWEK FDPDATQFIE FS KLSDFAA ALDPPLLIAK PNKVQLIAMD LPMVSGDRIH CLDILFAFTK RVLGESGEMD SLRSQMEERF MSANPSKVSY EPI TTTLKR KQEDVSATVI QRAYRRYRLR QNVKNISSIY IKDGDRDDDL LNKKDMAFDN VNENSSPEKT DATSSTTSPP SYDS VTKPD KEKYEQDRTE KEDKGKDSKE SKK

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 regulatory subunit beta-1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{...

MacromoleculeName: (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid
type: ligand / ID: 5 / Number of copies: 1 / Formula: UK0
Molecular weightTheoretical: 316.435 Da
Chemical component information

ChemComp-UK0:
(4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid

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Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #7: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 7 / Number of copies: 1 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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Macromolecule #8: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 8 / Number of copies: 10 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

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

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Macromolecule #9: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 9 / 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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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
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

33184

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220477
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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