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Yorodumi- EMDB-42491: CryoEM Structure of Allosterically Switchable De Novo Protein sr3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42491 | |||||||||
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Title | CryoEM Structure of Allosterically Switchable De Novo Protein sr312, in Open State with Effector Peptide | |||||||||
Map data | ||||||||||
Sample |
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Keywords | de novo / allosterically switchable de novo protein / sr312 / effector peptide / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Weidle C / Skotheim R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature Title: De novo design of allosterically switchable protein assemblies Authors: Pillai A / Idris A / Philomin A / Weidle C / Skotheim R / Leung PJY / Broerman A / Demakis C / Borst AJ / Praetorius F / Baker D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42491.map.gz | 27.3 MB | EMDB map data format | |
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Header (meta data) | emd-42491-v30.xml emd-42491.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42491_fsc.xml | 6.6 KB | Display | FSC data file |
Images | emd_42491.png | 110.1 KB | ||
Filedesc metadata | emd-42491.cif.gz | 6 KB | ||
Others | emd_42491_half_map_1.map.gz emd_42491_half_map_2.map.gz | 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42491 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42491 | HTTPS FTP |
-Validation report
Summary document | emd_42491_validation.pdf.gz | 692.8 KB | Display | EMDB validaton report |
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Full document | emd_42491_full_validation.pdf.gz | 692.3 KB | Display | |
Data in XML | emd_42491_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_42491_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42491 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42491 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42491.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_42491_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42491_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex is comprised of 4 sr312 proteins, each sr312 protein is b...
Entire | Name: Complex is comprised of 4 sr312 proteins, each sr312 protein is bound to an effector peptide, putting the protein in an open state. Complex is formed with C4 symmetry. |
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Components |
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-Supramolecule #1: Complex is comprised of 4 sr312 proteins, each sr312 protein is b...
Supramolecule | Name: Complex is comprised of 4 sr312 proteins, each sr312 protein is bound to an effector peptide, putting the protein in an open state. Complex is formed with C4 symmetry. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 206.1 KDa |
-Supramolecule #2: sr312 protein
Supramolecule | Name: sr312 protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #3: effector peptide
Supramolecule | Name: effector peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) / Synthetically produced: Yes |
-Macromolecule #1: sr312
Macromolecule | Name: sr312 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 47.297691 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGTVTFDITN IDWETAEWIM KHVYLIAKKE GTDVTFSFKE GELQITVKNL HEEAKREIEK WIRAAQLAQD PDAESKAEAR KILNELITE KAEELREKTK DEEVRELARE AARLALESDD IEVQRVVLKA LLAALKSKDE EVIRLLLLAA VLAAAAARSG S PEEKLEIA ...String: SGTVTFDITN IDWETAEWIM KHVYLIAKKE GTDVTFSFKE GELQITVKNL HEEAKREIEK WIRAAQLAQD PDAESKAEAR KILNELITE KAEELREKTK DEEVRELARE AARLALESDD IEVQRVVLKA LLAALKSKDE EVIRLLLLAA VLAAAAARSG S PEEKLEIA KKALELAMKS KDEEVIRLAL LAAVLAARSD DEEVLKKVKE ALEKMERIMD LEDVAREKSG SAEASQAVKE IA DIAEEAL REGLCEVARV ALKRLFKLAK DYPGSDVASL AKKALEKIAE TALRNGCKET AELAKLLLFL LLIIEVVLKM GVR MLTHRG GNAVIVVIEG LHPSQIVQLM QDVIKAAKKL GVTVTITVSG DIVVIMVVVG ASDEEQEEAR RLVQEIARAL QEAK RKGAN EEQLEQLLRE LLERAEREGG SG |
-Macromolecule #2: Effector peptide cs221B
Macromolecule | Name: Effector peptide cs221B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.091635 KDa |
Sequence | String: EERKKELAKE VIETAKKLIE KLAKEE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: 150 mM NaCl, 40 mM Tris, pH 8.0 | |||||||||
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3795 / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |