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- EMDB-33485: Nav1.7 mutant class2 -

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Basic information

Entry
Database: EMDB / ID: EMD-33485
TitleNav1.7 mutant class2
Map data
Sample
  • Complex: alpha1-beta1-beta2 ternary complex
    • 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: CHOLESTEROL HEMISUCCINATE
  • Ligand: CHOLESTEROL
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
Keywordsaction potential / 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 cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / regulation of sodium ion transmembrane transport ...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 cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / regulation of sodium ion transmembrane transport / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport / node of Ranvier / voltage-gated sodium channel complex / cardiac muscle cell action potential involved in contraction / locomotion / regulation of ventricular cardiac muscle cell membrane repolarization / sodium channel inhibitor activity / neuronal action potential propagation / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / detection of temperature stimulus involved in sensory perception of pain / behavioral response to pain / membrane depolarization / intercalated disc / sodium channel regulator activity / sodium ion transmembrane transport / cardiac muscle contraction / sensory perception of pain / 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 / nervous system development / gene expression / response to heat / 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 / 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 / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / 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 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: 2.8 Å
AuthorsHuang G / Wu Q / Li Z / Pan X / Yan N
Funding support United States, China, 2 items
OrganizationGrant numberCountry
Princeton UniversityShirley M. Tilghman endowed professorship United States
Beijing Municipal Science and Technology CommissionZ191100001119127 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na1.7.
Authors: Gaoxingyu Huang / Qiurong Wu / Zhangqiang Li / Xueqin Jin / Xiaoshuang Huang / Tong Wu / Xiaojing Pan / Nieng Yan /
Abstract: Voltage-gated sodium (Na) channel Na1.7 has been targeted for the development of nonaddictive pain killers. Structures of Na1.7 in distinct functional states will offer an advanced mechanistic ...Voltage-gated sodium (Na) channel Na1.7 has been targeted for the development of nonaddictive pain killers. Structures of Na1.7 in distinct functional states will offer an advanced mechanistic understanding and aid drug discovery. Here we report the cryoelectron microscopy analysis of a human Na1.7 variant that, with 11 rationally introduced point mutations, has a markedly right-shifted activation voltage curve with V reaching 69 mV. The voltage-sensing domain in the first repeat (VSD) in a 2.7-Å resolution structure displays a completely down (deactivated) conformation. Compared to the structure of WT Na1.7, three gating charge (GC) residues in VSD are transferred to the cytosolic side through a combination of helix unwinding and spiral sliding of S4 and ∼20° domain rotation. A conserved WNФФD motif on the cytoplasmic end of S3 stabilizes the down conformation of VSD. One GC residue is transferred in VSD mainly through helix sliding. Accompanying GC transfer in VSD and VSD, rearrangement and contraction of the intracellular gate is achieved through concerted movements of adjacent segments, including S4-5, S4-5, S5, and all S6 segments. Our studies provide important insight into the electromechanical coupling mechanism of the single-chain voltage-gated ion channels and afford molecular interpretations for a number of pain-associated mutations whose pathogenic mechanism cannot be revealed from previously reported Na structures.
History
DepositionMay 22, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33485.png

Downloads & links

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Map

FileDownload / File: emd_33485.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.)
1.08 Å/pix.
x 320 pix.
= 346.4 Å		1.08 Å/pix.
x 320 pix.
= 346.4 Å		1.08 Å/pix.
x 320 pix.
= 346.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.52
Minimum - Maximum-2.62973 - 5.0583854
Average (Standard dev.)0.006642129 (±0.08628989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33485_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_33485_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : alpha1-beta1-beta2 ternary complex

EntireName: alpha1-beta1-beta2 ternary complex
Components
  • Complex: alpha1-beta1-beta2 ternary complex
    • 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: CHOLESTEROL HEMISUCCINATE
  • Ligand: CHOLESTEROL
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Supramolecule #1: alpha1-beta1-beta2 ternary complex

SupramoleculeName: alpha1-beta1-beta2 ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 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: 230.599281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EKGGGARGGS GGGSWSHPQF EKGFDYKDDD DKGTMAMLPP PGPQSFVHFT KQSLALIEQR IAERKSKEPK EEKKDDDEEA PKPSSDLEA GKQLPFIYGD IPPGMVSEPL EDLDPYYADK KTFIVLNKGK TIFRFNATPA LYMLSPFSPL RRISIKILVH S LFSMLIMC ...String:
EKGGGARGGS GGGSWSHPQF EKGFDYKDDD DKGTMAMLPP PGPQSFVHFT KQSLALIEQR IAERKSKEPK EEKKDDDEEA PKPSSDLEA GKQLPFIYGD IPPGMVSEPL EDLDPYYADK KTFIVLNKGK TIFRFNATPA LYMLSPFSPL RRISIKILVH S LFSMLIMC TILTNCIFMT MNNPPDWTKN VKYTFTGIYT FESLVKILAR GFCVGEFTFL RDPWNWLDFV VIVFAYLTEF VN LGNVSAL RTFRVLRALK TISVIPGLKT IVGALIQSVK KLSDVMILTV FCLSVFALIG LQLFMGNLKH KCFRNSLENN ETL ESIMNT LESEEDFRKY FYYLEGSKDA LLCGFSTDSG QCPEGYTCVK IGRNPDYGYT SFDTFSWAFL ALFRLMTQDY WENL YQQTL RAAGKTYMIF FVVVIFLGSF YLINLILAVV AMAYEEQNQA NIEEAKQKEL EFQQMLDRLK KEQEEAEAIA AAAAE YTSI RRSRIMGLSE SSSETSKLSS KSAKERRNRR KKKNQKKLSS GEEKGDAEKL SKSESEDSIR RKSFHLGVEG HRRAHE KRL STPNQSPLSI RGSLFSARRS SRTSLFSFKG RGRDIGSETE FADDEHSIFG DNESRRGSLF VPHRPQERRS SNISQAS RS PPMLPVNGKM HSAVDCNGVV SLVDGRSALM LPNGQLLPEV IIDKATSDDS GTTNQIHKKR RCSSYLLSED MLNDPNLR Q RAMSRASILT NTVEELEESR QKCPPWWYRF AHKFLIWNCS PYWIKFKKCI YFIVMDPFVD LAITICIVLN TLFMAMEHH PMTEEFKNVL AIRNLVFTGI FAAEMVLKLI AMDPYEYFQV GWNIFDSLIV TLSLVELFLA DVEGLSVLRS FRLLRVFKLA KSWPTLNML IKIIGNSVGA FGNLMLVLFI IVFIFAVVGM QLFGKSYKEC VCKINDDCTL PRWHMNDFFH SFLIVFRVLC G EWIETMWD CMEVAGQAMC LIFYMMVFFI GNLVVLNLFL ALLLSSFSSD NLTAIEEDPD ANNLQIAVTR IKKGINYVKQ TL REFILKA FSKKPKISRE IRQAEDLNTK KENYISNHTL AEMSKGHNFL KEKDKISGFG SSVDKHLMED SDGQSFIHNP SLT VTVPIA PGESDLENMN AEELSSDSDS EYSKVRLNRS SSSECSTVDN PLPGEGEEAE AEPMNSDEPE ACFTDGCVWR FSCC QVNIE SGKGKIWWNI RKTCYKIVEH SWFESFIVLM ILLSSGALAF EDIYIERKKT IKIILEYADK IFTYIFILEM LLKWI AYGY KTYFTNAWCW LDFLIVDVSL VTLVANTLGY SDLGPIKSLR TLRALRPLRA LSRFEGMRVV VNALIGAIPS IMNVLL VCL IFWLIFSIMG VNLFAGKFYE CINTTDGSRF PASQVPNRSE CFALMNVSQN VRWKNLKVNF DNVGLGYLSL LQVATFK GW TIIMYAAVDS VNVDKQPKYE YSLYMYIYFI FFIIFGSFFT LNLFICVIID NFNQQKKKLG GQDIFMTEEQ KKYYNAMK K LGSKKPQKPI PRPGNKIQGC IFDLVTNQAF DISIMVLICL NMVTMMVEKE GQSQHMTEVL YWINVVFIIL FTGECVLKL ISLRHYYFTV GWNIFDFVVV IISIVGMFLA DLIETYFVSP TLFRVIRLAR IGRILRLVKG AKGIRTLLFA LMMSLPALFN IGLLLFLVM FIYAIFGMSN FAYVKKEDGI NDMFNFETFG NSMICLFQIT TSAGWDGLLA PILNSKPPDC DPKKVHPGSS V EGDCGNPS VGIFYFVSYI IISFLVVVNM YIAVILENFS VATEESTEPL SEDDFEMFYE VWEKFDPDAT QFIEFSKLSD FA AALDPPL LIAKPNKVQL IAMDLPMVSG DRIHCLDILF AFTKRVLGES GEMDSLRSQM EERFMSANPS KVSYEPITTT LKR KQEDVS ATVIQRAYRR YRLRQNVKNI SSIYIKDGDR DDDLLNKKDM AFDNVNENSS PEKTDATSST TSPPSYDSVT KPDK EKYEQ DRTEKEDKGK DSKESKK

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 #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 regulatory 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: 7 / 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: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 5 / 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

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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: 17 / 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: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen ...

MacromoleculeName: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
type: ligand / ID: 9 / Number of copies: 1 / Formula: 1PW
Molecular weightTheoretical: 421.508 Da
Chemical component information

ChemComp-1PW:
(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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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: 6 / 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: 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: 11 / Number of copies: 1 / 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

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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:

9781

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 394163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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