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- PDB-5h1q: C. elegans INX-6 gap junction hemichannel -

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Basic information

Entry
Database: PDB / ID: 5h1q
TitleC. elegans INX-6 gap junction hemichannel
ComponentsInnexin-6
KeywordsTRANSPORT PROTEIN / innexin / gap junction channel / octamer / wild type
Function / homologyInnexin / Innexin / Pannexin family profile. / gap junction hemi-channel activity / gap junction channel activity / gap junction / ion transport / integral component of membrane / plasma membrane / Innexin-6
Function and homology information
Specimen sourceCaenorhabditis elegans (roundworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsOshima, A. / Tani, K. / Fujiyoshi, Y.
CitationJournal: Nat Commun / Year: 2016
Title: Atomic structure of the innexin-6 gap junction channel determined by cryo-EM.
Authors: Atsunori Oshima / Kazutoshi Tani / Yoshinori Fujiyoshi
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 11, 2016 / Release: Dec 7, 2016
RevisionDateData content typeGroupProviderType
1.0Dec 7, 2016Structure modelrepositoryInitial release
1.1Feb 1, 2017Structure modelDatabase references
1.2Feb 15, 2017Structure modelOther

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Structure visualization

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Assembly

Deposited unit
A: Innexin-6
B: Innexin-6
C: Innexin-6
D: Innexin-6
E: Innexin-6
F: Innexin-6
G: Innexin-6
H: Innexin-6


Theoretical massNumber of molelcules
Total (without water)361,3908
Polyers361,3908
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)30690
ΔGint (kcal/M)-139
Surface area (Å2)134350

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Components

#1: Protein/peptide
Innexin-6 / / Protein opu-6


Mass: 45173.766 Da / Num. of mol.: 8 / Source: (gene. exp.) Caenorhabditis elegans (roundworm) / Gene: inx-6, opu-6, C36H8.2 / Plasmid name: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U3N4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: INX-6 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (roundworm)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFastBac1
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

MicroscopyMicroscope model: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 74398 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00824488
ELECTRON MICROSCOPYf_angle_d1.00133360
ELECTRON MICROSCOPYf_dihedral_angle_d11.15819408
ELECTRON MICROSCOPYf_chiral_restr0.0593680
ELECTRON MICROSCOPYf_plane_restr0.0054128

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