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- PDB-8j7m: ion channel -

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Basic information

Entry
Database: PDB / ID: 8j7m
Titleion channel
Componentsion 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)
KeywordsTRANSPORT PROTEIN / ion channel
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
CHOLESTEROL / Chem-POV / Green fluorescent protein / Voltage dependent ion channel
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen, H.W. / Chen, H.W.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)31971134 Brazil
CitationJournal: To Be Published
Title: ion channel
Authors: Chen, H.W. / Chen, H.W.
History
DepositionApr 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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),Voltage dependent ion channel,Green fluorescent protein (Fragment)
D: 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)
B: 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)
C: 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,95818
Polymers361,0514
Non-polymers6,90714
Water00
1


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

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Components

#1: Protein
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)


Mass: 90262.719 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: VDC1, gfp / Production host: Homo sapiens (human) / References: UniProt: R1FVI4, UniProt: A0A059PIQ0
#2: 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
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestN

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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 / Type: COMPLEX / Entity ID: #1 / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81844 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099276
ELECTRON MICROSCOPYf_angle_d0.92112644
ELECTRON MICROSCOPYf_dihedral_angle_d21.1243208
ELECTRON MICROSCOPYf_chiral_restr0.061388
ELECTRON MICROSCOPYf_plane_restr0.0061460

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