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- EMDB-33016: Ion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-33016
TitleIon channel
Map data
Sample
  • Complex: ion channel complex
    • Protein or peptide: ion channel,GFP-TwinStrep
  • Protein or peptide: ion channel
Keywordsion channel / TRANSPORT PROTEIN
Biological speciesEmiliania huxleyi (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsJiang D / Zhang J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Nat Commun / Year: 2022
Title: N-type fast inactivation of a eukaryotic voltage-gated sodium channel.
Authors: Jiangtao Zhang / Yiqiang Shi / Junping Fan / Huiwen Chen / Zhanyi Xia / Bo Huang / Juquan Jiang / Jianke Gong / Zhuo Huang / Daohua Jiang /
Abstract: Voltage-gated sodium (Na) channels initiate action potentials. Fast inactivation of Na channels, mediated by an Ile-Phe-Met motif, is crucial for preventing hyperexcitability and regulating firing ...Voltage-gated sodium (Na) channels initiate action potentials. Fast inactivation of Na channels, mediated by an Ile-Phe-Met motif, is crucial for preventing hyperexcitability and regulating firing frequency. Here we present cryo-electron microscopy structure of NaEh from the coccolithophore Emiliania huxleyi, which reveals an unexpected molecular gating mechanism for Na channel fast inactivation independent of the Ile-Phe-Met motif. An N-terminal helix of NaEh plugs into the open activation gate and blocks it. The binding pose of the helix is stabilized by multiple electrostatic interactions. Deletion of the helix or mutations blocking the electrostatic interactions completely abolished the fast inactivation. These strong interactions enable rapid inactivation, but also delay recovery from fast inactivation, which is ~160-fold slower than human Na channels. Together, our results provide mechanistic insights into fast inactivation of NaEh that fundamentally differs from the conventional local allosteric inhibition, revealing both surprising structural diversity and functional conservation of ion channel inactivation.
History
DepositionMar 5, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33016.png

Downloads & links

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Map

FileDownload / File: emd_33016.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.56
Minimum - Maximum-3.519802 - 5.0435066
Average (Standard dev.)0.0062239976 (±0.108883105)
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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Sample components

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Entire : ion channel complex

EntireName: ion channel complex
Components
  • Complex: ion channel complex
    • Protein or peptide: ion channel,GFP-TwinStrep
  • Protein or peptide: ion channel

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Supramolecule #1: ion channel complex

SupramoleculeName: ion channel complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Emiliania huxleyi (eukaryote)

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Macromolecule #1: ion channel,GFP-TwinStrep

MacromoleculeName: ion channel,GFP-TwinStrep / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Emiliania huxleyi (eukaryote)
Molecular weightTheoretical: 91.684469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIAAIHNARR KKREAAAAHK AQHRTAENSM DSLEDSTHET DAGERAQAGS TKLAWTDVVA PPPRKVVFWL PHQRKVFDFY ASQGVQYFT AFLIVSNFIF NCAEKEWDPY TDQLYQGLWR WGEFAFNTMF LIELLINFYG IAFCFWRYNW AWNTFDLVVV A IGTLTMAE ...String:
MIAAIHNARR KKREAAAAHK AQHRTAENSM DSLEDSTHET DAGERAQAGS TKLAWTDVVA PPPRKVVFWL PHQRKVFDFY ASQGVQYFT AFLIVSNFIF NCAEKEWDPY TDQLYQGLWR WGEFAFNTMF LIELLINFYG IAFCFWRYNW AWNTFDLVVV A IGTLTMAE AIGGNFMPPS MALIRNLRAF RIFRLFKRIK SLNKIIVSLG KAIPGVANAF VIMVIIMCIY AILGVEFYHM TG SDGTYVT YNDNVKRGLC TGDEVELGQC SLNQTVSSET ARGYTYGEEY YGTFFRALYT LFQVLTGESW SEAVARPAVF ESH YDSFGP VLFYVSFIII CQIVLINVVV AVLLDKMVEE DDSEDPEKQT VAEKLSEMLS QEHAQLREIF RTWDEDNSGT ISIK EWRKA VKSMGYRGPI DVLDQIFASM DKDHSGELDY AEIDRMLSPT AARERRSSTH ANPKRSVKEE VVAMRAEFTD HVARL ETQI AALVLELQLQ RKPCGAEAPA PAHSRLAHDS DGAPTEPPPP AAPDHHHLED DEDTTQRVAA ALEVLFQGPS KGEELF TGV VPILVELDGD VNGHKFSVRG EGEGDATNGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKRH DFFKSAM PE GYVQERTISF KDDGTYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNFNSHNV YITADKQKNG IKANFKIR H NVEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSVLSK DPNEKRDHMV LLEFVTAAGI THGMDEWSHP QFEKGGGSG GGSGGSAWSH PQFEK

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Macromolecule #2: ion channel

MacromoleculeName: ion channel / type: protein_or_peptide / ID: 2 / Details: N-terminal helix of either of the four protomers / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Emiliania huxleyi (eukaryote)
Molecular weightTheoretical: 1.913298 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIAAIHNARR KKREAAA

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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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61065
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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