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- EMDB-67991: The structure of Nav1.7 with veratridine standing near the IFM mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-67991
TitleThe structure of Nav1.7 with veratridine standing near the IFM motif (site I)
Map data
Sample
  • Complex: Nav1.7-veratridine complex
    • Protein or peptide: Sodium channel regulatory subunit beta-1
    • Protein or peptide: Sodium channel regulatory subunit beta-2
    • Protein or peptide: Sodium channel protein type 9 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: Veratridine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate
KeywordsNav1.7 / voltage gated sodium channel / cryo-EM / veratridine / site I / MEMBRANE PROTEIN
Function / homology
Function and homology information


response to pyrethroid / corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / action potential propagation / detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction ...response to pyrethroid / corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / action potential propagation / detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / 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 / axon initial segment / 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 / neuronal action potential propagation / locomotion / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / detection of temperature stimulus involved in sensory perception of pain / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / behavioral response to pain / intercalated disc / sodium channel regulator activity / membrane depolarization / neuronal action potential / cardiac muscle contraction / T-tubule / sensory perception of pain / axon terminus / axon guidance / sodium ion transmembrane transport / post-embryonic development / circadian rhythm / positive regulation of neuron projection development / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / nervous system development / response to heat / gene expression / chemical synaptic transmission / perikaryon / 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 / 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 ...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 / 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 subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Sodium channel regulatory subunit beta-2 / 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: 2.7 Å
AuthorsFan X / Huang J / Yan N
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000754/2020-L France
CitationJournal: To Be Published
Title: Open-state structure of veratridine-activated human Nav1.7 reveals the molecular choreography of fast inactivation
Authors: Fan X / Chen J / Xue L / Wang H / Wu T / Huang X / Lu F / Jin X / Song C / Huang J / Yan N
History
DepositionDec 24, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67991.jpg

Downloads & links

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Map

FileDownload / File: emd_67991.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 356.48 Å		1.11 Å/pix.
x 320 pix.
= 356.48 Å		1.11 Å/pix.
x 320 pix.
= 356.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-4.582863 - 6.9159346
Average (Standard dev.)-0.005791647 (±0.13462864)
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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Half map: #2

Fileemd_67991_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_67991_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 : Nav1.7-veratridine complex

EntireName: Nav1.7-veratridine complex
Components
  • Complex: Nav1.7-veratridine complex
    • Protein or peptide: Sodium channel regulatory subunit beta-1
    • Protein or peptide: Sodium channel regulatory subunit beta-2
    • Protein or peptide: Sodium channel protein type 9 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: Veratridine
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • 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: Nav1.7-veratridine complex

SupramoleculeName: Nav1.7-veratridine complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium channel regulatory subunit beta-1

MacromoleculeName: Sodium channel regulatory subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.206018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GCVEVDSETE AVYGMTFKIL CISCKRRSET NAETFTEWTF RQKGTEEFVK ILRYENEVLQ LEEDERFEGR VVWNGSRGTK DLQDLSIFI TNVTYNHSGD YECHVYRLLF FENYEHNTSV VKKIHIEVVD KANRDMASIV SEIMMYVLIV VLTIWLVAEM I YCYKKIAA ATETA

UniProtKB: Sodium channel regulatory subunit beta-1

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Macromolecule #2: Sodium channel regulatory subunit beta-2

MacromoleculeName: Sodium channel regulatory subunit beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.965937 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEVTVPATLN VLNGSDARLP CTFNSCYTVN HKQFSLNWTY QECNNCSEEM FLQFRMKIIN LKLERFQDRV EFSGNPSKYD VSVMLRNVQ PEDEGIYNCY IMNPPDRHRG HGKIHLQVLM

UniProtKB: Sodium channel regulatory subunit beta-2

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Macromolecule #3: Sodium channel protein type 9 subunit alpha

MacromoleculeName: Sodium channel protein type 9 subunit alpha / type: protein_or_peptide / ID: 3 / 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 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 #6: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 8 / Formula: LPE
Molecular weightTheoretical: 510.708 Da
Chemical component information

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

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Macromolecule #7: Veratridine

MacromoleculeName: Veratridine / type: ligand / ID: 7 / Number of copies: 1 / Formula: A1E26
Molecular weightTheoretical: 673.79 Da

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Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 2 / 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: (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: 10 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 335177
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 335177
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #3

Image processing ID3
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 335177
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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