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Yorodumi- PDB-8gnb: structure of human connexin 40.1 side-by-side decamer channel by ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gnb | ||||||||||||
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Title | structure of human connexin 40.1 side-by-side decamer channel by cryoEM | ||||||||||||
Components | Gap junction delta-4 protein | ||||||||||||
Keywords | MEMBRANE PROTEIN / connexin side-by-side decamer channel | ||||||||||||
Function / homology | Function and homology information regulation of satellite cell activation involved in skeletal muscle regeneration / connexin complex / Gap junction assembly / gap junction channel activity / cell-cell signaling Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Zhang, H. / Wang, D.P. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: structure of human connexin 40.1 side-by-side decamer channel by cryoEM Authors: Zhang, H. / Wang, D.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gnb.cif.gz | 410.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gnb.ent.gz | 284.2 KB | Display | PDB format |
PDBx/mmJSON format | 8gnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gnb_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8gnb_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8gnb_validation.xml.gz | 67.2 KB | Display | |
Data in CIF | 8gnb_validation.cif.gz | 89.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/8gnb ftp://data.pdbj.org/pub/pdb/validation_reports/gn/8gnb | HTTPS FTP |
-Related structure data
Related structure data | 34159MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 227 / Label seq-ID: 3 - 227
NCS oper:
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-Components
#1: Protein | Mass: 26030.973 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GJD4, CX40.1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96KN9 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: structure of human connexin 40.1 side-by-side decamer channel Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.26 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106770 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 147.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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