[English] 日本語
Yorodumi
- EMDB-63108: Complex of voltage-gated sodium channel NavPaS from American cock... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63108
TitleComplex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and sea anemone toxin Av3
Map data
Sample
  • Complex: Complex structure of voltage-gated sodium channel NavPas with sea anemone toxin Av3
    • Complex: Sodium channel protein PaFPC1
      • Protein or peptide: Sodium channel protein PaFPC1
    • Complex: sea anemone toxin Av3
      • Protein or peptide: Delta-actitoxin-Avd2a
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsComplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


nematocyst / 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 / toxin activity / extracellular region
Similarity search - Function
Neurotoxin 3, Anemonia / Neurotoxin 3, Actiniidae / Neurotoxin 3 superfamily / Anemonia sulcata toxin III family / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage gated sodium channel, alpha subunit / 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 / Delta-actitoxin-Avd2a
Similarity search - Component
Biological speciesPeriplaneta americana (American cockroach) / Anemonia sulcata (snake-locks sea anemone)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsJiang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32372580 China
CitationJournal: To Be Published
Title: Structure of voltage-gated sodium channel NavPas and sea anemone toxin Av3
Authors: Jiang H
History
DepositionJan 13, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63108.png

Downloads & links

-
Map

FileDownload / File: emd_63108.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66
Minimum - Maximum-2.5081518 - 3.9293804
Average (Standard dev.)-0.00016195104 (±0.060547013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_63108_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63108_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex structure of voltage-gated sodium channel NavPas with sea...

EntireName: Complex structure of voltage-gated sodium channel NavPas with sea anemone toxin Av3
Components
  • Complex: Complex structure of voltage-gated sodium channel NavPas with sea anemone toxin Av3
    • Complex: Sodium channel protein PaFPC1
      • Protein or peptide: Sodium channel protein PaFPC1
    • Complex: sea anemone toxin Av3
      • Protein or peptide: Delta-actitoxin-Avd2a
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

-
Supramolecule #1: Complex structure of voltage-gated sodium channel NavPas with sea...

SupramoleculeName: Complex structure of voltage-gated sodium channel NavPas with sea anemone toxin Av3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Periplaneta americana (American cockroach)

-
Supramolecule #2: Sodium channel protein PaFPC1

SupramoleculeName: Sodium channel protein PaFPC1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Periplaneta americana (American cockroach)

-
Supramolecule #3: sea anemone toxin Av3

SupramoleculeName: sea anemone toxin Av3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Anemonia sulcata (snake-locks sea anemone)

-
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

-
Macromolecule #2: Delta-actitoxin-Avd2a

MacromoleculeName: Delta-actitoxin-Avd2a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anemonia sulcata (snake-locks sea anemone)
Molecular weightTheoretical: 2.940362 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSCCPCYWGG CPWGQNCYPE GCSGPKV

UniProtKB: Delta-actitoxin-Avd2a

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #6: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
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: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 353627
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more