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- EMDB-6770: Structure of the Nav1.4-beta1 complex from electric eel -

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Basic information

Entry
Database: EMDB / ID: EMD-6770
TitleStructure of the Nav1.4-beta1 complex from electric eel
Map dataexperimental map
Sample
  • Organelle or cellular component: voltage gated sodium channel EeNav1.4
    • Protein or peptide: Sodium channel protein
    • Protein or peptide: Voltage-gated sodium channel beta subunit 1
  • Ligand: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine
  • Ligand: BETA-D-MANNOSE
Function / homology
Function and homology information


voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex / sodium channel activity / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / sodium channel regulator activity
Similarity search - Function
Sodium channel subunit beta-1/beta-3 / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ion transport domain / Ion transport protein ...Sodium channel subunit beta-1/beta-3 / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ion transport domain / Ion transport protein / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Voltage-gated sodium channel beta subunit 1 / Sodium channel protein
Similarity search - Component
Biological speciesElectrophorus electricus (electric eel) / Electric eel (electric eel)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsYan Z / Zhou Q / Wu JP / Yan N
CitationJournal: Cell / Year: 2017
Title: Structure of the Na1.4-β1 Complex from Electric Eel.
Authors: Zhen Yan / Qiang Zhou / Lin Wang / Jianping Wu / Yanyu Zhao / Gaoxingyu Huang / Wei Peng / Huaizong Shen / Jianlin Lei / Nieng Yan /
Abstract: Voltage-gated sodium (Na) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa1.4, the Na channel from electric eel, in complex with the β1 subunit at 4. ...Voltage-gated sodium (Na) channels initiate and propagate action potentials. Here, we present the cryo-EM structure of EeNa1.4, the Na channel from electric eel, in complex with the β1 subunit at 4.0 Å resolution. The immunoglobulin domain of β1 docks onto the extracellular L5 and L6 loops of EeNa1.4 via extensive polar interactions, and the single transmembrane helix interacts with the third voltage-sensing domain (VSD). The VSDs exhibit "up" conformations, while the intracellular gate of the pore domain is kept open by a digitonin-like molecule. Structural comparison with closed NaPaS shows that the outward transfer of gating charges is coupled to the iris-like pore domain dilation through intricate force transmissions involving multiple channel segments. The IFM fast inactivation motif on the III-IV linker is plugged into the corner enclosed by the outer S4-S5 and inner S6 segments in repeats III and IV, suggesting a potential allosteric blocking mechanism for fast inactivation.
History
DepositionJun 15, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseAug 9, 2017-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5xsy
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6770.png

Downloads & links

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Map

FileDownload / File: emd_6770.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationexperimental map
Voxel sizeX=Y=Z: 1.338 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.22568451 - 0.33369038
Average (Standard dev.)0.0012356095 (±0.013148039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 267.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z267.600267.600267.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2260.3340.001

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Supplemental data

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Half map: half map1

Fileemd_6770_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_6770_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : voltage gated sodium channel EeNav1.4

EntireName: voltage gated sodium channel EeNav1.4
Components
  • Organelle or cellular component: voltage gated sodium channel EeNav1.4
    • Protein or peptide: Sodium channel protein
    • Protein or peptide: Voltage-gated sodium channel beta subunit 1
  • Ligand: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine
  • Ligand: BETA-D-MANNOSE

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Supramolecule #1: voltage gated sodium channel EeNav1.4

SupramoleculeName: voltage gated sodium channel EeNav1.4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Electrophorus electricus (electric eel)

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Macromolecule #1: Sodium channel protein

MacromoleculeName: Sodium channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Electric eel (electric eel)
Molecular weightTheoretical: 208.519797 KDa
SequenceString: MARKFSSARP EMFRRFTPDS LEEIEAFTEL KKSCTLEKKE PESTPRIDLE AGKPLPMIYG DPPEDLLNIP LEDLDPFYKT QKTFIVISK GNIINRFNAE RALYIFSPFN PIRRGAIRVF VNSAFNFFIM FTIFSNCIFM TISNPPAWSK IVEYTFTGIY T FEVIVKVL ...String:
MARKFSSARP EMFRRFTPDS LEEIEAFTEL KKSCTLEKKE PESTPRIDLE AGKPLPMIYG DPPEDLLNIP LEDLDPFYKT QKTFIVISK GNIINRFNAE RALYIFSPFN PIRRGAIRVF VNSAFNFFIM FTIFSNCIFM TISNPPAWSK IVEYTFTGIY T FEVIVKVL SRGFCIGHFT FLRDPWNWLD FSVVTMTYIT EFIDLRNVSA LRTFRVLRAL KTITIFPGLK TIVRALIESM KQ MGDVVIL TVFSLAVFTL AGMQLFMGNL RHKCIRWPIS NVTLDYESAY NTTFDFTAYI ENEENQYFLD GALDALLCGN NSD AGKCPE GYTCMKAGRN PNYGYTNYDN FAWTFLCLFR LMLQDYWENL YQMTLRAAGK SYMVFFIMVI FLGSFYLINL ILAV VAMAY EEQNQATLAE AQEKEAEFQR AVEQLRIQQE QINDERKASL ASQLTQNQEA EITDDGDDAI KECNGKAFPL ANIRE PSSV KLSTEEQRSD SKSMDSKHSV DKPSLKHKAA STMSVFTLED LEAARRPCPP VWYKFAGFVF KWNCCGPWVF LKKWVH FVM MDPFTDLFIT LCIILNTLFM SIEHHPMNES FQSLLSAGNL VFTTIFAAEM VLKIIALDPY YYFQQTWNIF DSIIVSL SL LELGLSNMQG MSVLRSLRLL RIFKLAKSWP TLNILIKIIC NSVGALGNLT IVLAIIVFIF ALVGFQLFGK NYKEYVCK I SDDCELPRWH MNDFFHSFLI VFRALCGEWI ETMWDCMEVG GVPMCLAVYM MVIIIGNLVM LNLFLALLLS SFSSDNLSS IEEDDEVNSL QVASERISRA KNWVKIFITG TVQALVLWIQ GKKPPSDDVV GEEGDNEGKK DTLPLNYLDG EKIVDGITNC VESPTLNLP IVKGESEIEE EGLVDSSDEE DTNKKKHALN DEDSSVCSTV DYSPSEQDPL AKEEEEEEEE EPEELESKDP E ACFTEKCI WRFPFLDVDI TQGKGKIWWN LRRTCYTIVE HDYFETFIIF MILLSSGVLA FEDIYIWRRR VIKVILEYAD KV FTYVFIV EMLLKWVAYG FKRYFTDAWC WLDFVIVGAS IMGITSSLLG YEELGAIKNL RTIRALRPLR ALSRFEGMKV VVR ALLGAI PSIMNVLLVC LMFWLIFSIM GVNLFAGKFY RCINTTTDEI LPVEEVNNRS DCMALMYTNE VRWVNLKVNY DNAG MGYLS LLQVSTFKGW MDIMYAAVDS REVEDQPIYE INVYMYLYFV IFIVFGAFFT LNLFIGVIID NFNRQKQKLG GEDLF MTEE QKKYYNAMKK LGSKKAAKCI PRPSNVVQGV VYDIVTQPFT DIFIMALICI NMVAMMVESE DQSQVKKDIL SQINVI FVI IFTVECLLKL LALRQYFFTV GWNVFDFAVV VISIIGLLLS DIIEKYFVSP TLFRVIRLAR IARVLRLIRA AKGIRTL LF ALMMSLPALF NIGLLLFLIM FIFSIFGMSN FAYVKKQGGV DDIFNFETFG NSMICLFEIT TSAGWDGLLL PTLNTGPP D CDPDVENPGT DVRGNCGNPG KGITFFCSYI ILSFLVVVNM YIAIILENFG VAQEESSDLL CEDDFVMFDE TWHKFDVHG TQFLDYNDLP RFVNALQEPM RIPNPNRHKL AKMDMYVVME DKISYLDVLL AVTQEVLGDT TEMEAMRLSI QAKFKKDNPS PTFFEPVVT TLRRKEEEWA SVVIQRAFRQ YLLMRAVSHA SFLSQIKHMN EGPKDGVGSQ DSLITQKMNA LYRGNPELTM P LEQQIKPM LDKPRMPSLS VPETYPIQIP KEVTNEVILH SAPMVRQNYS YSGAIVVRES IV

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Macromolecule #2: Voltage-gated sodium channel beta subunit 1

MacromoleculeName: Voltage-gated sodium channel beta subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Electric eel (electric eel)
Molecular weightTheoretical: 23.657322 KDa
SequenceString: MSAVQLLWMP VVLCVMQGRL SNGACVEVDS DTEAVVGHGF KLGCISCKMR GEVQASATVD WWFMAKGESE FSHIYSYIDM TGMVNDERF LDRLNWMGSK NTFDLQDGSI YILNVTLNDT GTYRCYFDRT LTFNYYEFRT NINKTITLNV VPKATRGTAS I LSEVMMYV ...String:
MSAVQLLWMP VVLCVMQGRL SNGACVEVDS DTEAVVGHGF KLGCISCKMR GEVQASATVD WWFMAKGESE FSHIYSYIDM TGMVNDERF LDRLNWMGSK NTFDLQDGSI YILNVTLNDT GTYRCYFDRT LTFNYYEFRT NINKTITLNV VPKATRGTAS I LSEVMMYV SIIGLQLWLL VEMVYCYRKI AAAGEEALRE SAAKPPLKLH P

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Macromolecule #3: N-ACETYL-D-GLUCOSAMINE

MacromoleculeName: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 3 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da

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Macromolecule #4: BETA-D-MANNOSE

MacromoleculeName: BETA-D-MANNOSE / type: ligand / ID: 4 / Number of copies: 6 / Formula: BMA
Molecular weightTheoretical: 180.156 Da

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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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.2 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6698

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123431

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