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- EMDB-33296: Sodium channel -

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Basic information

Entry
Database: EMDB / ID: EMD-33296
TitleSodium channel
Map data
Sample
  • Complex: Sodium channel
    • Protein or peptide: Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein
    • Protein or peptide: Sodium channel subunit beta-1,Green fluorescent protein
    • Protein or peptide: Sodium channel subunit beta-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid
KeywordsSodium channel / PROTEIN TRANSPORT
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) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsJiang DH / Zhang JT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structural basis for Na1.7 inhibition by pore blockers.
Authors: Jiangtao Zhang / Yiqiang Shi / Zhuo Huang / Yue Li / Bei Yang / Jianke Gong / Daohua Jiang /
Abstract: Voltage-gated sodium channel Na1.7 plays essential roles in pain and odor perception. Na1.7 variants cause pain disorders. Accordingly, Na1.7 has elicited extensive attention in developing new ...Voltage-gated sodium channel Na1.7 plays essential roles in pain and odor perception. Na1.7 variants cause pain disorders. Accordingly, Na1.7 has elicited extensive attention in developing new analgesics. Here we present cryo-EM structures of human Na1.7/β1/β2 complexed with inhibitors XEN907, TC-N1752 and Na1.7-IN2, explaining specific binding sites and modulation mechanism for the pore blockers. These inhibitors bind in the central cavity blocking ion permeation, but engage different parts of the cavity wall. XEN907 directly causes α- to π-helix transition of DIV-S6 helix, which tightens the fast inactivation gate. TC-N1752 induces π-helix transition of DII-S6 helix mediated by a conserved asparagine on DIII-S6, which closes the activation gate. Na1.7-IN2 serves as a pore blocker without causing conformational change. Electrophysiological results demonstrate that XEN907 and TC-N1752 stabilize Na1.7 in inactivated state and delay the recovery from inactivation. Our results provide structural framework for Na1.7 modulation by pore blockers, and important implications for developing subtype-selective analgesics.
History
DepositionApr 25, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33296.png

Downloads & links

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Map

FileDownload / File: emd_33296.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.376
Minimum - Maximum-3.007206 - 4.571147
Average (Standard dev.)0.0047792736 (±0.09395932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33296_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33296_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Sodium channel

EntireName: Sodium channel
Components
  • Complex: Sodium channel
    • Protein or peptide: Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein
    • Protein or peptide: Sodium channel subunit beta-1,Green fluorescent protein
    • Protein or peptide: Sodium channel subunit beta-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid

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Supramolecule #1: Sodium channel

SupramoleculeName: Sodium channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fl...

MacromoleculeName: Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein
type: protein_or_peptide / ID: 1
Details: The fusion protein of Sodium channel, linker, GFP, and tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 255.679906 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 QLLPEGTTNQ IHKKRRCSSY LLSEDMLNDP NLRQRAMSRA SILTNTVEEL EESRQKCPPW WYRFAHKFLI WNCSPYWI K FKKCIYFIVM DPFVDLAITI CIVLNTLFMA MEHHPMTEEF KNVLAIGNLV FTGIFAAEMV LKLIAMDPYE YFQVGWNIF DSLIVTLSLV ELFLADVEGL SVLRSFRLLR VFKLAKSWPT LNMLIKIIGN SVGALGNLTL VLAIIVFIFA VVGMQLFGKS YKECVCKIN DDCTLPRWHM NDFFHSFLIV FRVLCGEWIE TMWDCMEVAG QAMCLIVYMM VMVIGNLVVL NLFLALLLSS F SSDNLTAI EEDPDANNLQ IAVTRIKKGI NYVKQTLREF ILKAFSKKPK ISREIRQAED LNTKKENYIS NHTLAEMSKG HN FLKEKDK ISGFGSSVDK HLMEDSDGQS FIHNPSLTVT VPIAPGESDL ENMNAEELSS DSDSEYSKVR LNRSSSSECS TVD NPLPGE GEEAEAEPMN SDEPEACFTD GCVRRFSCCQ VNIESGKGKI WWNIRKTCYK IVEHSWFESF IVLMILLSSG ALAF EDIYI ERKKTIKIIL EYADKIFTYI FILEMLLKWI AYGYKTYFTN AWCWLDFLIV DVSLVTLVAN TLGYSDLGPI KSLRT LRAL RPLRALSRFE GMRVVVNALI GAIPSIMNVL LVCLIFWLIF SIMGVNLFAG KFYECINTTD GSRFPASQVP NRSECF ALM NVSQNVRWKN LKVNFDNVGL GYLSLLQVAT FKGWTIIMYA AVDSVNVDKQ PKYEYSLYMY IYFVVFIIFG SFFTLNL FI GVIIDNFNQQ KKKLGGQDIF MTEEQKKYYN AMKKLGSKKP QKPIPRPGNK IQGCIFDLVT NQAFDISIMV LICLNMVT M MVEKEGQSQH MTEVLYWINV VFIILFTGEC VLKLISLRHY YFTVGWNIFD FVVVIISIVG MFLADLIETY FVSPTLFRV IRLARIGRIL RLVKGAKGIR TLLFALMMSL PALFNIGLLL FLVMFIYAIF GMSNFAYVKK EDGINDMFNF ETFGNSMICL FQITTSAGW DGLLAPILNS KPPDCDPKKV HPGSSVEGDC GNPSVGIFYF VSYIIISFLV VVNMYIAVIL ENFSVATEES T EPLSEDDF EMFYEVWEKF DPDATQFIEF SKLSDFAAAL DPPLLIAKPN KVQLIAMDLP MVSGDRIHCL DILFAFTKRV LG ESGEMDS LRSQMEERFM SANPSKVSYE PITTTLKRKQ EDVSATVIQR AYRRYRLRQN VKNISSIYIK DGDRDDDLLN KKD MAFDNV NENSSPEKTD ATSSTTSPPS YDSVTKPDKE KYEQDRTEKE DKGKDSKESK KAAALEVLFQ GPSKGEELFT GVVP ILVEL DGDVNGHKFS VRGEGEGDAT NGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYPDHM KRHDFFKSAM PEGYV QERT ISFKDDGTYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNFNS HNVYITADKQ KNGIKANFKI RHNVED GSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSV LSKDPNEKRD HMVLLEFVTA AGITHGMDEW SHPQFEKGGG SGGGSGG SA WSHPQFEK

UniProtKB: Sodium channel protein type 9 subunit alpha

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Macromolecule #2: Sodium channel subunit beta-1,Green fluorescent protein

MacromoleculeName: Sodium channel subunit beta-1,Green fluorescent protein
type: protein_or_peptide / ID: 2
Details: The fusion protein of Sodium channel, linker, GFP, and tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 54.472129 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 AAALEVLFQG PSKGEELFTG VV PILVELD GDVNGHKFSV RGEGEGDATN GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK RHDFFKSAMP EGY VQERTI SFKDDGTYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNFNSH NVYITADKQK NGIKANFKIR HNVE DGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSVL SKDPNEKRDH MVLLEFVTAA GITHGMDEHH HHHHHHHHDY KDDDD K

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: 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 #6: (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)ph...

MacromoleculeName: (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid
type: ligand / ID: 6 / Number of copies: 1 / Formula: G4I
Molecular weightTheoretical: 516.515 Da
Chemical component information

ChemComp-G4I:
(1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid

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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 K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9782

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158142
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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