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- EMDB-36042: ion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-36042
Titleion channel
Map data
Sample
  • Complex: ion channel
    • Protein or peptide: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
Keywordsion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Voltage-gated cation channel calcium and sodium / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Green fluorescent protein / Voltage dependent ion channel
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen HW / Jiang D
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)31971134 Brazil
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 15, 2024-
Map releaseMay 15, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36042.png

Downloads & links

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Map

FileDownload / File: emd_36042.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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.423
Minimum - Maximum-4.126518 - 6.7497845
Average (Standard dev.)0.0044387225 (±0.12753554)
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: #1

Fileemd_36042_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36042_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : ion channel

EntireName: ion channel
Components
  • Complex: ion channel
    • Protein or peptide: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL

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Supramolecule #1: ion channel

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

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Macromolecule #1: ion channel,Voltage dependent ion channel,Green fluorescent prote...

MacromoleculeName: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 90.262719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEAAAAHKAQ HRTAENSMDS LEDSTHETDA GERAQAGSTK LAWTDVVAPP PRKVVFWLPH QRKVFDFYAS QGVQYFTAFL IVSNFIFNC AEKEWDPYTD QLYQGLWRWG EFAFNTMFLI ELLINFYGIA FCFWRYNWAW NTFDLVVVAI GTLTMAEAIG G NFMPPSMA ...String:
MEAAAAHKAQ HRTAENSMDS LEDSTHETDA GERAQAGSTK LAWTDVVAPP PRKVVFWLPH QRKVFDFYAS QGVQYFTAFL IVSNFIFNC AEKEWDPYTD QLYQGLWRWG EFAFNTMFLI ELLINFYGIA FCFWRYNWAW NTFDLVVVAI GTLTMAEAIG G NFMPPSMA LIRNLRAFRI FRLFKRIKSL NKIIVSLGKA IPGVANAFVI MVIIMCIYAI LGVEFYHMTG SDGTYVTYND NV KRGLCTG DEVELGQCSL NQTVSSETAR GYTYGEEYYG TFFRALYTLF QVLTGESWSE AVARPAVFES HYDSFGPVLF YVS FIIICQ IVLINVVVAV LLDKMVEEDD SEDPEKQTVA EKLSEMLSQE HAQLREIFRT WDEDNSGTIS IKEWRKAVKS MGYR GPIDV LDQIFASMDK DHSGELDYAE IDRMLSPTAA RERRSSTHAN PKRSVKEEVV AMRAEFTDHV ARLETQIAAL VLELQ LQRK PCGAEAPAPA HSRLAHDSDG APTEPPPPAA PDHHHLEDDE DTTQRVAAAL EVLFQGPSKG EELFTGVVPI LVELDG DVN GHKFSVRGEG EGDATNGKLT LKFICTTGKL PVPWPTLVTT LTYGVQCFSR YPDHMKRHDF FKSAMPEGYV QERTISF KD DGTYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNFNSHNVYI TADKQKNGIK ANFKIRHNVE DGSVQLAD H YQQNTPIGDG PVLLPDNHYL STQSVLSKDP NEKRDHMVLL EFVTAAGITH GMDEWSHPQF EKGGGSGGGS GGSAWSHPQ FEK

UniProtKB: Voltage dependent ion channel, Green fluorescent protein

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 10 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81844
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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