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- EMDB-60867: Nav1.7 with mutations that eliminate beta1 binding -

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Basic information

Entry
Database: EMDB / ID: EMD-60867
TitleNav1.7 with mutations that eliminate beta1 binding
Map dataNav1.7 with mutations that eliminate beta1 binding
Sample
  • Complex: Nav1.7 with mutations that eliminate beta1 binding
    • Protein or peptide: Sodium channel protein type 9 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: SODIUM ION
  • 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: CHOLESTEROL HEMISUCCINATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
KeywordsVoltage-gated sodium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


action potential propagation / detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / node of Ranvier / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / behavioral response to pain ...action potential propagation / detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / node of Ranvier / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / behavioral response to pain / neuronal action potential / axon terminus / sensory perception of pain / sodium ion transmembrane transport / post-embryonic development / circadian rhythm / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / inflammatory response / axon / plasma membrane
Similarity search - Function
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-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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein type 9 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsYan N / Li Z / Wu T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32330052 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Critical role of extracellular loops in differential modulations of TTX-sensitive and TTX-resistant Na channels.
Authors: Tong Wu / Xinyu Yang / Xueqin Jin / Nieng Yan / Zhangqiang Li /
Abstract: The cardiac voltage-gated sodium channel Na1.5 is resistant to tetrodotoxin (TTXr). Here, we report a cryo-electron microscopy (cryo-EM) structure of wild-type human Na1.5, coexpressed with the β1 ...The cardiac voltage-gated sodium channel Na1.5 is resistant to tetrodotoxin (TTXr). Here, we report a cryo-electron microscopy (cryo-EM) structure of wild-type human Na1.5, coexpressed with the β1 auxiliary subunit and treated with high-concentration TTX, at 3.4 Å resolution. Structural comparison reveals the molecular determinants for the distinct responses to TTX as well as β subunits between TTXr and TTX-sensitive (TTXs) Na channels. A conserved cation-π interaction between the guanidinium group of TTX and Tyr or Phe on the P2 helix in TTXs Na channels is lost in all TTXr subtypes owing to the replacement by Cys/Ser at the corresponding locus, explaining their differential TTX sensitivities. The β1 subunit is invisible in the EM map. Comparison of Na1.5 with Na1.7 and Na1.8, which are, respectively, TTXs and TTXr, identifies four sites on the extracellular loops (ECLs) that may account for their different β1-binding abilities. When the corresponding residues in TTXs Na1.7 are replaced with those from Na1.5, the modulatory effects of β1 on channel activation and inactivation are diminished. Consistently, β1 is absent in the 3D EM reconstruction of this Na1.7 mutant. Together with our previous structure-guided discovery that TTXr channels lack a Cys on the ECL for disulfide bond formation with β2 or β4, the structure-function relationship studies underscore the importance of the ECLs in the mechanistic distinctions between TTXs and TTXr Na channels. The ECLs may be further explored for the development of subtype-specific drugs.
History
DepositionJul 20, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60867.png

Downloads & links

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Map

FileDownload / File: emd_60867.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNav1.7 with mutations that eliminate beta1 binding
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.236
Minimum - Maximum-2.4427173 - 3.9293475
Average (Standard dev.)0.00016264732 (±0.08215399)
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: half A

Fileemd_60867_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_60867_half_map_2.map
Annotationhalf B
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 with mutations that eliminate beta1 binding

EntireName: Nav1.7 with mutations that eliminate beta1 binding
Components
  • Complex: Nav1.7 with mutations that eliminate beta1 binding
    • Protein or peptide: Sodium channel protein type 9 subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: SODIUM ION
  • 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: CHOLESTEROL HEMISUCCINATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en

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Supramolecule #1: Nav1.7 with mutations that eliminate beta1 binding

SupramoleculeName: Nav1.7 with mutations that eliminate beta1 binding / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 231.137781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMAMLPPP GPQSFVHFTK QSLALIEQRI AERKSKEPKE EKKDDDEEA PKPSSDLEAG KQLPFIYGDI PPGMVSEPLE DLDPYYADKK TFIVLNKGKT IFRFNATPAL YMLSPFSPLR R ISIKILVH ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMAMLPPP GPQSFVHFTK QSLALIEQRI AERKSKEPKE EKKDDDEEA PKPSSDLEAG KQLPFIYGDI PPGMVSEPLE DLDPYYADKK TFIVLNKGKT IFRFNATPAL YMLSPFSPLR R ISIKILVH SLFSMLIMCT ILTNCIFMTM NNPPDWTKNV EYTFTGIYTF ESLVKILARG FCVGEFTFLR DPWNWLDFVV IV FAYLTEF VNLGNVSALR TFRVLRALKT ISVIPGLKTI VGALIQSVKK LSDVMILTVF CLSVFALIGL QLFMGNLKHK CFR NSLENN ETLESIMNTL ESEEDFRKYF LYLEGSKDAL LCGFSTDSGQ CPEGYTCVKI GRNPDYGYTS FDTFSWAFLA LFRL MTQDY WERLYQQTLR AAGKTYMIFF VVVIFLGSFY LINLILAVVA MAYEEQNQAN IEEAKQKELE FQQMLDRLKK EQEEA EAIA AAAAEYTSIR RSRIMGLSES SSETSKLSSK SAKERRNRRK KKNQKKLSSG EEKGDAEKLS KSESEDSIRR KSFHLG VEG HRRAHEKRLS TPNQSPLSIR GSLFSARRSS RTSLFSFKGR GRDIGSETEF ADDEHSIFGD NESRRGSLFV PHRPQER RS SNISQASRSP PMLPVNGKMH SAVDCNGVVS LVDGRSALML PNGQLLPEVI IDKATSDDSG TTNQIHKKRR CSSYLLSE D MLNDPNLRQR AMSRASILTN TVEELEESRQ KCPPWWYRFA HKFLIWNCSP YWIKFKKCIY FIVMDPFVDL AITICIVLN TLFMAMEHHP MTEEFKNVLA IGNLVFTGIF AAEMVLKLIA MDPYEYFQVG WNIFDSLIVT LSLVELFLAD VEGLSVLRSF RLLRVFKLA KSWPTLNMLI KIIGNSVGAL GNLTLVLAII VFIFAVVGMQ LFGKSYKECV CKINDDCTLP RWHMNDFFHS F LIVFRVLC GEWIETMWDC MEVAGQAMCL IVYMMVMVIG NLVVLNLFLA LLLSSFSSDN LTAIEEDPDA NNLQIAVTRI KK GINYVKQ TLREFILKAF SKKPKISREI RQAEDLNTKK ENYISNHTLA EMSKGHNFLK EKDKISGFGS SVDKHLMEDS DGQ SFIHNP SLTVTVPIAP GESDLENMNA EELSSDSDSE YSKVRLNRSS SSECSTVDNP LPGEGEEAEA EPMNSDEPEA CFTD GCVWR FSCCQVNIES GKGKIWWNIR KTCYKIVEHS WFESFIVLMI LLSSGALAFE DIYIERKKTI KIILEYADKI FTYIF ILEM LLKWIAYGYK TYFTNAWCWL DFLIVDVSLV TLVANTLGYS DLGPIKSLRT LRALRPLRAL SRFEGMRVVV NALIGA IPS IMNVLLVCLI FWLIFSIMGV NLFAGKFYEC INTTDGSRFP ASQVPNRSEC FALMNVSQNV RWKNLKVNFD NVGLGYL SL LQVATFKGWT IIMYAAVDSV NVDKQPKYEY SLYMYIYFVV FIIFGSFFTL NLFIGVIIDN FNQQKKKLGG QDIFMTEE Q KKYYNAMKKL GSKKPQKPIP RPGNKIQGCI FDLVTNQAFD ISIMVLICLN MVTMMVEKEG QSQHMTEVLY WINVVFIIL FTGECVLKLI SLRHYYFTVG WNIFDFVVVI ISIVGMFLAD LIETYFVSPT LFRVIRLARI GRILRLVKGA KGIRTLLFAL MMSLPALFN IGLLLFLVMF IYAIFGMSNF AYVKWEDGIN DMFNFETFGN SMICLFQITT SAGWDGLLAP ILNSKPPDCD P TLPNSNGS RGDCGNPSVG IFYFVSYIII SFLVVVNMYI AVILENFSVA TEESTEPLSE DDFEMFYEVW EKFDPDATQF IE FSKLSDF AAALDPPLLI AKPNKVQLIA MDLPMVSGDR IHCLDILFAF TKRVLGESGE MDSLRSQMEE RFMSANPSKV SYE PITTTL KRKQEDVSAT VIQRAYRRYR LRQNVKNISS IYIKDGDRDD DLLNKKDMAF DNVNENSSPE KTDATSSTTS PPSY DSVTK PDKEKYEQDR TEKEDKGKDS KESKK

UniProtKB: Sodium channel protein type 9 subunit alpha

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: 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: 4 / 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

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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: 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 #7: (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: 7 / 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 #8: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 8 / Number of copies: 5 / 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 #9: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 9 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #10: (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: 10 / 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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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: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193309
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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