+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36039 | |||||||||
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Title | ion channel | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ion channel / TRANSPORT PROTEIN | |||||||||
Function / homology | Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / plasma membrane / Ion transport domain-containing protein Function and homology information | |||||||||
Biological species | Homo sapiens (human) / Aequorea victoria (jellyfish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Chen HW | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: structure of ion channel Authors: Chen HW / Chen HW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36039.map.gz | 118.1 MB | EMDB map data format | |
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Header (meta data) | emd-36039-v30.xml emd-36039.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
Images | emd_36039.png | 37.9 KB | ||
Filedesc metadata | emd-36039.cif.gz | 5.5 KB | ||
Others | emd_36039_half_map_1.map.gz emd_36039_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36039 | HTTPS FTP |
-Validation report
Summary document | emd_36039_validation.pdf.gz | 802.9 KB | Display | EMDB validaton report |
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Full document | emd_36039_full_validation.pdf.gz | 802.5 KB | Display | |
Data in XML | emd_36039_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_36039_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36039 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36039 | HTTPS FTP |
-Related structure data
Related structure data | 8j7fMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36039.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36039_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36039_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ion channel complex
Entire | Name: ion channel complex |
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Components |
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-Supramolecule #1: ion channel complex
Supramolecule | Name: ion channel complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: ion channel,Voltage dependent ion channel,Green fluorescent prote...
Macromolecule | Name: ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Ion transport domain-containing protein type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Aequorea victoria (jellyfish) |
Molecular weight | Theoretical: 33.237289 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: WLPHQRKVFD FYASQGVQYF TAFLIVSNFI FNCAEKEWDP YTDQLYQGLW RWGEFAFNTM FLIELLINFY GIAFCFWRYN WAWNTFDLV VVAIGTLTMA EAIGGNFMPP SMALIRNLRA FRIFRLFKRI KSLNKIIVSL GKAIPGVANA FVIMVIIMCI Y AILGVEFY ...String: WLPHQRKVFD FYASQGVQYF TAFLIVSNFI FNCAEKEWDP YTDQLYQGLW RWGEFAFNTM FLIELLINFY GIAFCFWRYN WAWNTFDLV VVAIGTLTMA EAIGGNFMPP SMALIRNLRA FRIFRLFKRI KSLNKIIVSL GKAIPGVANA FVIMVIIMCI Y AILGVEFY HMTGSDGTYV TYNDNVKRGL CTGDEVELGQ CSLNQTVSSE TARGYTYGEE YYGTFFRALY TLFQVLTGES WS EAVARPA VFESHYDSFG PVLFYVSFII ICQIVLINVV VAVLLDKMVE ED UniProtKB: Ion transport domain-containing protein |
-Macromolecule #2: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-A...
Macromolecule | Name: ILE-ALA-ALA-ILE-HIS-ASN-ALA-ARG-ARG-LYS-LYS-ARG-GLU-ALA-ALA-ALA-ALA-HIS-LYS-ALA type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 2.191584 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: IAAIHNARRK KREAAAAHKA |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 4 / Number of copies: 4 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #5: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 12 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 10 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: 60.0 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: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110665 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |