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Yorodumi- EMDB-30712: Cryo-Molecular electron tomography of epidermal growth factor rec... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30712 | |||||||||
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Title | Cryo-Molecular electron tomography of epidermal growth factor receptor (averaged cluster 1) | |||||||||
Map data | Unliganded EGFR, averaged cluster 1 | |||||||||
Sample |
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Biological species | EGFR (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 15.0 Å | |||||||||
Authors | Purba ER / Saita E-I / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN | |||||||||
Citation | Journal: To Be Published Title: Conformational flexibility transitions of the epidermal growth factor receptor dimer upon activation Authors: Purba ER / Saita E-I / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30712.map.gz | 4.2 MB | EMDB map data format | |
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Header (meta data) | emd-30712-v30.xml emd-30712.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_30712.png | 12.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30712 | HTTPS FTP |
-Validation report
Summary document | emd_30712_validation.pdf.gz | 302.4 KB | Display | EMDB validaton report |
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Full document | emd_30712_full_validation.pdf.gz | 302 KB | Display | |
Data in XML | emd_30712_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30712 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30712.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unliganded EGFR, averaged cluster 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.258 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Unliganded EGFR
Entire | Name: Unliganded EGFR |
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Components |
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-Supramolecule #1: Unliganded EGFR
Supramolecule | Name: Unliganded EGFR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Unliganded EGFR, subtomogram averaged cluster 1 |
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Source (natural) | Organism: EGFR (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: DH5a / Recombinant cell: E. coli / Recombinant plasmid: pIRES2-ZsGreen1-Thr-His8 |
Molecular weight | Theoretical: 300 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 20.0 0.5 / Component - Name: Tris-HCL Details: Solutions were made fresh from concentrated to avoid microbial contamination. |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I / Details: Blot for 5.5 seconds before plunging. |
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Phase plate: OTHER |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 2258 pixel / Digitization - Dimensions - Height: 2258 pixel / Average exposure time: 1.8 sec. / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 37000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: -2.0 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
-Atomic model buiding 2
Initial model | PDB ID: |
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Refinement | Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
-Atomic model buiding 3
Initial model | PDB ID: |
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Refinement | Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |