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- EMDB-29082: Cryo-EM structure of human voltage-gated sodium channel Nav1.6 -

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Entry
Database: EMDB / ID: EMD-29082
TitleCryo-EM structure of human voltage-gated sodium channel Nav1.6
Map dataCryo-EM structure of human voltage-gated sodium channel Nav1.6
Sample
  • Complex: Complex of human voltage-gated sodium channel Nav1.6 with auxiliary beta-1 subunit
    • Protein or peptide: Sodium channel protein type 8 subunit alpha
    • Protein or peptide: Sodium channel subunit beta-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CHOLESTEROL
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate
Function / homology
Function and homology information


corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / 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 / axon initial segment / sodium ion binding / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction ...corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / 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 / axon initial segment / sodium ion binding / 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 / peripheral nervous system development / node of Ranvier / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity / locomotion / optic nerve development / 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 / parallel fiber to Purkinje cell synapse / sodium ion transport / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / calcium ion import across plasma membrane / membrane depolarization / neuronal action potential / sodium ion transmembrane transport / sodium channel regulator activity / intercalated disc / presynaptic active zone membrane / cardiac muscle contraction / T-tubule / myelination / axon guidance / postsynaptic density membrane / positive regulation of neuron projection development / Sensory perception of sweet, bitter, and umami (glutamate) taste / Z disc / cell junction / nervous system development / perikaryon / cytoplasmic vesicle / transmembrane transporter binding / cell adhesion / axon / glutamatergic synapse / extracellular region / ATP binding / membrane / plasma membrane
Similarity search - Function
Voltage gated sodium channel, alpha-8 subunit / Sodium channel subunit beta-1/beta-3 / 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 / IQ calmodulin-binding motif / Voltage-gated cation channel calcium and sodium ...Voltage gated sodium channel, alpha-8 subunit / Sodium channel subunit beta-1/beta-3 / 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 / IQ calmodulin-binding motif / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / 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 subunit beta-1 / Sodium channel protein type 8 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFan X / Huang J / Yan N
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000754 France
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Cryo-EM structure of human voltage-gated sodium channel Na1.6.
Authors: Xiao Fan / Jian Huang / Xueqin Jin / Nieng Yan /
Abstract: Voltage-gated sodium channel Na1.6 plays a crucial role in neuronal firing in the central nervous system (CNS). Aberrant function of Na1.6 may lead to epilepsy and other neurological disorders. ...Voltage-gated sodium channel Na1.6 plays a crucial role in neuronal firing in the central nervous system (CNS). Aberrant function of Na1.6 may lead to epilepsy and other neurological disorders. Specific inhibitors of Na1.6 thus have therapeutic potentials. Here we present the cryo-EM structure of human Na1.6 in the presence of auxiliary subunits β1 and fibroblast growth factor homologous factor 2B (FHF2B) at an overall resolution of 3.1 Å. The overall structure represents an inactivated state with closed pore domain (PD) and all "up" voltage-sensing domains. A conserved carbohydrate-aromatic interaction involving Trp302 and Asn326, together with the β1 subunit, stabilizes the extracellular loop in repeat I. Apart from regular lipids that are resolved in the EM map, an unprecedented Y-shaped density that belongs to an unidentified molecule binds to the PD, revealing a potential site for developing Na1.6-specific blockers. Structural mapping of disease-related Na1.6 mutations provides insights into their pathogenic mechanism.
History
DepositionDec 14, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29082.png

Downloads & links

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Map

FileDownload / File: emd_29082.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human voltage-gated sodium channel Nav1.6
Voxel sizeX=Y=Z: 1.114 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.069776 - 4.038702
Average (Standard dev.)-0.002144974 (±0.09334062)
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_29082_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_29082_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_29082_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human voltage-gated sodium channel Nav1.6 with auxilia...

EntireName: Complex of human voltage-gated sodium channel Nav1.6 with auxiliary beta-1 subunit
Components
  • Complex: Complex of human voltage-gated sodium channel Nav1.6 with auxiliary beta-1 subunit
    • Protein or peptide: Sodium channel protein type 8 subunit alpha
    • Protein or peptide: Sodium channel subunit beta-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CHOLESTEROL
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate

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Supramolecule #1: Complex of human voltage-gated sodium channel Nav1.6 with auxilia...

SupramoleculeName: Complex of human voltage-gated sodium channel Nav1.6 with auxiliary beta-1 subunit
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium channel protein type 8 subunit alpha

MacromoleculeName: Sodium channel protein type 8 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 225.520609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAARLLAPPG PDSFKPFTPE SLANIERRIA ESKLKKPPKA DGSHREDDED SKPKPNSDLE AGKSLPFIYG DIPQGLVAVP LEDFDPYYL TQKTFVVLNR GKTLFRFSAT PALYILSPFN LIRRIAIKIL IHSVFSMIIM CTILTNCVFM TFSNPPDWSK N VEYTFTGI ...String:
MAARLLAPPG PDSFKPFTPE SLANIERRIA ESKLKKPPKA DGSHREDDED SKPKPNSDLE AGKSLPFIYG DIPQGLVAVP LEDFDPYYL TQKTFVVLNR GKTLFRFSAT PALYILSPFN LIRRIAIKIL IHSVFSMIIM CTILTNCVFM TFSNPPDWSK N VEYTFTGI YTFESLVKII ARGFCIDGFT FLRDPWNWLD FSVIMMAYIT EFVNLGNVSA LRTFRVLRAL KTISVIPGLK TI VGALIQS VKKLSDVMIL TVFCLSVFAL IGLQLFMGNL RNKCVVWPIN FNESYLENGT KGFDWEEYIN NKTNFYTVPG MLE PLLCGN SSDAGQCPEG YQCMKAGRNP NYGYTSFDTF SWAFLALFRL MTQDYWENLY QLTLRAAGKT YMIFFVLVIF VGSF YLVNL ILAVVAMAYE EQNQATLEEA EQKEAEFKAM LEQLKKQQEE AQAAAMATSA GTVSEDAIEE EGEEGGGSPR SSSEI SKLS SKSAKERRNR RKKRKQKELS EGEEKGDPEK VFKSESEDGM RRKAFRLPDN RIGRKFSIMN QSLLSIPGSP FLSRHN SKS SIFSFRGPGR FRDPGSENEF ADDEHSTVEE SEGRRDSLFI PIRARERRSS YSGYSGYSQG SRSSRIFPSL RRSVKRN ST VDCNGVVSLI GGPGSHIGGR LLPEATTEVE IKKKGPGSLL VSMDQLASYG RKDRINSIMS VVTNTLVEEL EESQRKCP P CWYKFANTFL IWECHPYWIK LKEIVNLIVM DPFVDLAITI CIVLNTLFMA MEHHPMTPQF EHVLAVGNLV FTGIFTAEM FLKLIAMDPY YYFQEGWNIF DGFIVSLSLM ELSLADVEGL SVLRSFRLLR VFKLAKSWPT LNMLIKIIGN SVGALGNLTL VLAIIVFIF AVVGMQLFGK SYKECVCKIN QDCELPRWHM HDFFHSFLIV FRVLCGEWIE TMWDCMEVAG QAMCLIVFMM V MVIGNLVV LNLFLALLLS SFSADNLAAT DDDGEMNNLQ ISVIRIKKGV AWTKLKVHAF MQAHFKQREA DEVKPLDELY EK KANCIAN HTGADIHRNG DFQKNGNGTT SGIGSSVEKY IIDEDHMSFI NNPNLTVRVP IAVGESDFEN LNTEDVSSES DPE GSKDKL DDTSSSEGST IDIKPEVEEV PVEQPEEYLD PDACFTEGCV QRFKCCQVNI EEGLGKSWWI LRKTCFLIVE HNWF ETFII FMILLSSGAL AFEDIYIEQR KTIRTILEYA DKVFTYIFIL EMLLKWTAYG FVKFFTNAWC WLDFLIVAVS LVSLI ANAL GYSELGAIKS LRTLRALRPL RALSRFEGMR VVVNALVGAI PSIMNVLLVC LIFWLIFSIM GVNLFAGKYH YCFNET SEI RFEIEDVNNK TECEKLMEGN NTEIRWKNVK INFDNVGAGY LALLQVATFK GWMDIMYAAV DSRKPDEQPK YEDNIYM YI YFVIFIIFGS FFTLNLFIGV IIDNFNQQKK KFGGQDIFMT EEQKKYYNAM KKLGSKKPQK PIPRPLNKIQ GIVFDFVT Q QAFDIVIMML ICLNMVTMMV ETDTQSKQME NILYWINLVF VIFFTCECVL KMFALRHYYF TIGWNIFDFV VVILSIVGM FLADIIEKYF VSPTLFRVIR LARIGRILRL IKGAKGIRTL LFALMMSLPA LFNIGLLLFL VMFIFSIFGM SNFAYVKHEA GIDDMFNFE TFGNSMICLF QITTSAGWDG LLLPILNRPP DCSLDKEHPG SGFKGDCGNP SVGIFFFVSY IIISFLIVVN M YIAIILEN FSVATEESAD PLSEDDFETF YEIWEKFDPD ATQFIEYCKL ADFADALEHP LRVPKPNTIE LIAMDLPMVS GD RIHCLDI LFAFTKRVLG DSGELDILRQ QMEERFVASN PSKVSYEPIT TTLRRKQEEV SAVVLQRAYR GHLARRGFIC KKT TSNKLE NGGTHREKKE STPSTASLPS YDSVTKPEKE KQQRAEEGRR ERAKRQKEVR ESKC

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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

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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: 7 / 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: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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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: 5 / 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: 3 / 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 #10: 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: 10 / Number of copies: 2 / 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 #11: (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: 11 / 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 #12: (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20la...

MacromoleculeName: (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate
type: ligand / ID: 12 / Number of copies: 1 / Formula: P3X
Molecular weightTheoretical: 661.89 Da
Chemical component information

ChemComp-P3X:
(5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate

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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

Concentration7 mg/mL
BufferpH: 7.5 / Details: 25 mM Tris-HCl (pH 7.5), 150 mM NaCl and 0.02% GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV

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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 / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 3168 / Average exposure time: 5.6 sec. / 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
Details: Initial 3D reference generated by Ab initio reconstruction
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 2
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74103
FSC plot (resolution estimation)

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