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- EMDB-63189: Complex of voltage-gated sodium channel NavPaS from American cock... -

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Basic information

Entry
Database: EMDB / ID: EMD-63189
TitleComplex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT
Map data
Sample
  • Complex: Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT
    • Complex: Sodium channel protein PaFPC
      • Protein or peptide: Sodium channel protein PaFPC1
    • Complex: scorpion alpha toxin LqhaIT
      • Protein or peptide: Alpha-insect toxin LqhaIT
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordssodium channel / alpha toxin / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane depolarization during action potential / voltage-gated sodium channel complex / sodium channel inhibitor activity / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / neuronal action potential / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage gated sodium channel, alpha subunit ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage gated sodium channel, alpha subunit / Knottin, scorpion toxin-like superfamily / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Sodium channel protein PaFPC1 / Alpha-insect toxin LqhaIT
Similarity search - Component
Biological speciesPeriplaneta americana (American cockroach) / Leiurus hebraeus (scorpion)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsJiang H / Xu HQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32372580 China
CitationJournal: To Be Published
Title: Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT
Authors: Jiang H / Xu HQ
History
DepositionJan 17, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63189.png

Downloads & links

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Map

FileDownload / File: emd_63189.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321.6 Å		1.07 Å/pix.
x 300 pix.
= 321.6 Å		1.07 Å/pix.
x 300 pix.
= 321.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.137267 - 5.9000287
Average (Standard dev.)0.009013814 (±0.11270594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63189_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_63189_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 : Complex of voltage-gated sodium channel NavPaS from American cock...

EntireName: Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT
Components
  • Complex: Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT
    • Complex: Sodium channel protein PaFPC
      • Protein or peptide: Sodium channel protein PaFPC1
    • Complex: scorpion alpha toxin LqhaIT
      • Protein or peptide: Alpha-insect toxin LqhaIT
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of voltage-gated sodium channel NavPaS from American cock...

SupramoleculeName: Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and scorpion alpha toxin LqhaIT
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Sodium channel protein PaFPC

SupramoleculeName: Sodium channel protein PaFPC / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Periplaneta americana (American cockroach)

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Supramolecule #3: scorpion alpha toxin LqhaIT

SupramoleculeName: scorpion alpha toxin LqhaIT / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Leiurus hebraeus (scorpion)

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Macromolecule #1: Sodium channel protein PaFPC1

MacromoleculeName: Sodium channel protein PaFPC1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Periplaneta americana (American cockroach)
Molecular weightTheoretical: 183.875422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMADNSPL IREERQRLFR PYTRAMLTAP SAQPAKENGK TEENKDNSR DKGRGANKDR DGSAHPDQAL EQGSRLPARM RNIFPAELAS TPLEDFDPFY KNKKTFVVVT KAGDIFRFSG E KSLWMLDP ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMADNSPL IREERQRLFR PYTRAMLTAP SAQPAKENGK TEENKDNSR DKGRGANKDR DGSAHPDQAL EQGSRLPARM RNIFPAELAS TPLEDFDPFY KNKKTFVVVT KAGDIFRFSG E KSLWMLDP FTPIRRVAIS TMVQPIFSYF IMITILIHCI FMIMPATQTT YILELVFLSI YTIEVVVKVL ARGFILHPFA YL RDPWNWL DFLVTLIGYI TLVVDLGHLY ALRAFRVLRS WRTVTIVPGW RTIVDALSLS ITSLKDLVLL LLFSLFVFAV LGL QIYMGV LTQKCVKHFP ADGSWGNFTD ERWFNYTSNS SHWYIPDDWI EYPLCGNSSG AGMCPPGYTC LQGYGGNPNY GYTS FDTFG WAFLSVFRLV TLDYWEDLYQ LALRSAGPWH ILFFIIVVFY GTFCFLNFIL AVVVMSYTHM VKRADEEKAA ERELK KEKK AASVANNTAN GQEQTTIEMN GDEAVVIDNN DQAARQQSDP ETPAPSVTQR LTDFLCVWDC CVPWQKLQGA IGAVVL SPF FELFIAVIIV LNITFMALDH HDMNIEFERI LRTGNYIFTS IYIVEAVLKI IALSPKFYFK DSWNVFDFII VVFAILE LG LEGVQGLSVF RSFRLLRVFR LAKFWPTLNN FMSVMTKSYG AFVNVMYVMF LLLFIFAIIG MQLFGMNYID NMERFPDG D LPRWNFTDFL HSFMIVFRAL CGEWIESMWD CMLVGDWSCI PFFVAVFFVG NLVILNLLIA LLLNNYGSFC TSPTSDEED SKDEDALAQI VRIFKRFKPN LNAVKLSPMK PDSEDIVESQ EIQGNNIADA EDVLAGEFPP DCCCNAFYKC FPSRPARDSS VQRMWSNIR RVCFLLAKNK YFQKFVTAVL VITSVLLALE DIYLPQRPVL VNITLYVDYV LTAFFVIEMI IMLFAVGFKK Y FTSKWYWL DFIVVVAYLL NFVLMCAGIE ALQTLRLLRV FRLFRPLSKV NGMQVVTSTL VEAVPHIFNV ILVGIFFWLV FA IMGVQLF AGKFYKCVDE NSTVLSHEIT MDRNDCLHEN YTWENSPMNF DHVGNAYLSL LQVATFKGWL QIMNDAIDSR EVH KQPIRE TNIYMYLYFI FFIVFGSFFI LKLFVCILID IFRQQRRKAE GLSATDSRTQ LIYRRAVMRT MSAKPVKRIP KPTC HPQSL MYDISVNRKF EYTMMILIIL NVAVMAIDHY GQSMEFSEVL DYLNLIFIII FFVECVIKVS GLRHHYFKDP WNIID FLYV VLAIAGLMLS DVIEKYFISP TLLRILRILR VGRLLRYFQS ARGMRLLLLA LRKALRTLFN VSFLLFVIMF VYAVFG MEF FMHIRDAGAI DDVYNFKTFG QSIILLFQLA TSAGWDGVYF AIANEEDCRA PDHELGYPGN CGSRALGIAY LVSYLII TC LVVINMYAAV ILDYVLEVYE DSKEGLTDDD YDMFFEVWQQ FDPEATQYIR YDQLSELLEA LQPPLQVQKP NKYKILSM N IPICKDDHIF YKDVLEALVK DVFSRRGSPV EAGDVQAPNV DEAEYKPVSS TLQRQREEYC VRLIQNAWRK HKQQN

UniProtKB: Sodium channel protein PaFPC1

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Macromolecule #2: Alpha-insect toxin LqhaIT

MacromoleculeName: Alpha-insect toxin LqhaIT / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leiurus hebraeus (scorpion)
Molecular weightTheoretical: 7.532585 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VRDAYIAKNY NCVYECFRDA YCNELCTKNG ASSGYCQWAG KYGNACWCYA LPDNVPIRVP GKCHRK

UniProtKB: Alpha-insect toxin LqhaIT

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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 K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: PDB ENTRY
PDB model - PDB ID:

5x0m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 483207
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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