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- PDB-8j7f: ion channel -

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Basic information

Entry
Database: PDB / ID: 8j7f
Titleion channel
Components
  • ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA
  • ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein
KeywordsTRANSPORT PROTEIN / ion channel
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / CHOLESTEROL / Chem-POV / Ion transport domain-containing protein
Function and homology information
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChen, H.W. / Jiang, D.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0May 15, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 15, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_admin / em_author_list / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
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Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein
B: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein
C: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein
D: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein
E: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,98125
Polymers135,1415
Non-polymers7,84020
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Protein
ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein


Mass: 33237.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: EMIHUDRAFT_123816, gfp / Production host: Homo sapiens (human) / References: UniProt: R1EKX3
#2: Protein/peptide ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA


Mass: 2191.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 30 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H46O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ion channel complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110665 / Symmetry type: POINT

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