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Yorodumi- EMDB-34156: structure of human connexin 40.1 intercellular gap junction chann... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34156 | ||||||||||||
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Title | structure of human connexin 40.1 intercellular gap junction channel by cryoEM | ||||||||||||
Map data | density map | ||||||||||||
Sample |
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Keywords | intercellular gap junction channel / MEMBRANE PROTEIN | ||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
Authors | Zhang H / Wang DP | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: structure of human connexin 40.1 intercellular gap junction channel by cryoEM Authors: Zhang H / Wang DP | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34156.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-34156-v30.xml emd-34156.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34156_fsc.xml | 17.5 KB | Display | FSC data file |
Images | emd_34156.png | 62.4 KB | ||
Others | emd_34156_half_map_1.map.gz emd_34156_half_map_2.map.gz | 200.5 MB 200.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34156 | HTTPS FTP |
-Validation report
Summary document | emd_34156_validation.pdf.gz | 930 KB | Display | EMDB validaton report |
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Full document | emd_34156_full_validation.pdf.gz | 929.6 KB | Display | |
Data in XML | emd_34156_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_34156_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34156 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34156 | HTTPS FTP |
-Related structure data
Related structure data | 8gn7MC 8gn8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34156.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | density map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_34156_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_34156_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : decameric structure of human connexin 40.1 intercellular gap junc...
Entire | Name: decameric structure of human connexin 40.1 intercellular gap junction channel |
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Components |
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-Supramolecule #1: decameric structure of human connexin 40.1 intercellular gap junc...
Supramolecule | Name: decameric structure of human connexin 40.1 intercellular gap junction channel type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 260 KDa |
-Macromolecule #1: Gap junction delta-4 protein
Macromolecule | Name: Gap junction delta-4 protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.030973 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEGVDLLGFL IITLNCNVTM VGKLWFVLTM LLRMLVIVLA GRPVYQDEQE RFVCNTLQPG CANVCYDVFS PVSHLRFWLI QGVCVLLPS AVFSVYVLHR GATLAALGPR RCPDPREPAS GQRRCPRPFG ERGGLQVPDF SAGYIIHLLL RTLLEAAFGA L HYFLFGFL ...String: MEGVDLLGFL IITLNCNVTM VGKLWFVLTM LLRMLVIVLA GRPVYQDEQE RFVCNTLQPG CANVCYDVFS PVSHLRFWLI QGVCVLLPS AVFSVYVLHR GATLAALGPR RCPDPREPAS GQRRCPRPFG ERGGLQVPDF SAGYIIHLLL RTLLEAAFGA L HYFLFGFL APKKFPCTRP PCTGVVDCYV SRPTEKSLLM LFLWAVSALS FLLGLADLVC SLRRRMRRRP GPPTS UniProtKB: Gap junction delta-4 protein |
-Macromolecule #2: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 30 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #3: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 10 / Formula: PTY |
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Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ChemComp-PTY: |
-Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Macromolecule | Name: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 10 / Formula: 3PE |
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Molecular weight | Theoretical: 748.065 Da |
Chemical component information | ChemComp-3PE: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |