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- EMDB-36041: ion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-36041
Titleion channel
Map data
Sample
  • Complex: ion channel complex
    • Protein or peptide: ion channel
    • Protein or peptide: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA
  • Ligand: water
Keywordsion channel / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen HW / Jiang D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural mechanism of voltage-gated sodium channel slow inactivation.
Authors: Huiwen Chen / Zhanyi Xia / Jie Dong / Bo Huang / Jiangtao Zhang / Feng Zhou / Rui Yan / Yiqiang Shi / Jianke Gong / Juquan Jiang / Zhuo Huang / Daohua Jiang /
Abstract: Voltage-gated sodium (Na) channels mediate a plethora of electrical activities. Na channels govern cellular excitability in response to depolarizing stimuli. Inactivation is an intrinsic property of ...Voltage-gated sodium (Na) channels mediate a plethora of electrical activities. Na channels govern cellular excitability in response to depolarizing stimuli. Inactivation is an intrinsic property of Na channels that regulates cellular excitability by controlling the channel availability. The fast inactivation, mediated by the Ile-Phe-Met (IFM) motif and the N-terminal helix (N-helix), has been well-characterized. However, the molecular mechanism underlying Na channel slow inactivation remains elusive. Here, we demonstrate that the removal of the N-helix of NaEh (NaEh) results in a slow-inactivated channel, and present cryo-EM structure of NaEh in a potential slow-inactivated state. The structure features a closed activation gate and a dilated selectivity filter (SF), indicating that the upper SF and the inner gate could serve as a gate for slow inactivation. In comparison to the NaEh structure, NaEh undergoes marked conformational shifts on the intracellular side. Together, our results provide important mechanistic insights into Na channel slow inactivation.
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36041.png

Downloads & links

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Map

FileDownload / File: emd_36041.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: 0.509
Minimum - Maximum-2.8521066 - 3.6245275
Average (Standard dev.)-0.00028983993 (±0.07871888)
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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Half map: #2

Fileemd_36041_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_36041_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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
    • Protein or peptide: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA
  • Ligand: water

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Supramolecule #1: ion channel complex

SupramoleculeName: ion channel complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ion channel

MacromoleculeName: ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-A...

MacromoleculeName: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.191584 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IAAIHNARRK KREAAAAHKA

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59377
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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