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Yorodumi- EMDB-42542: CryoEM Structure of Allosterically Switchable De Novo Protein sr3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42542 | |||||||||
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Title | CryoEM Structure of Allosterically Switchable De Novo Protein sr322, In Closed State without Effector Peptide, off Target Multimeric State | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Allosterically Switchable Protein / sr322 / closed state / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.32 Å | |||||||||
Authors | Weidle C / Borst A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024 Title: De Novo Design of Allosterically Switchable Protein Assemblies Authors: Pillai A / Idris A / Philomin A / Weidle C / Skotheim R / Leung P / 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_42542.map.gz | 27.3 MB | EMDB map data format | |
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Header (meta data) | emd-42542-v30.xml emd-42542.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42542_fsc.xml | 6.6 KB | Display | FSC data file |
Images | emd_42542.png | 81.5 KB | ||
Filedesc metadata | emd-42542.cif.gz | 6 KB | ||
Others | emd_42542_half_map_1.map.gz emd_42542_half_map_2.map.gz | 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42542 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42542 | HTTPS FTP |
-Validation report
Summary document | emd_42542_validation.pdf.gz | 653.7 KB | Display | EMDB validaton report |
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Full document | emd_42542_full_validation.pdf.gz | 653.3 KB | Display | |
Data in XML | emd_42542_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_42542_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42542 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42542 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42542.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: 1.68 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42542_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42542_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : sr322
Entire | Name: sr322 |
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Components |
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-Supramolecule #1: sr322
Supramolecule | Name: sr322 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Complex is made up of 4 monomeric proteins, and is purified as a 4 sided multimer sr322. In this structure two copies of sr322 interact in an off target way. |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 326.592 KDa |
-Macromolecule #1: de novo protein sr322
Macromolecule | Name: de novo protein sr322 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 40.089242 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGTVTFDITN ISHKAIDIIL KVVLGIAEHE GTEVTFHSER GQLQIEVKNL HEEDKRLIEQ AIEAARLADS PDPESVARAV ELLTKVAKA STNTELIQFI VKELLELARK LTDPKDLAKV LDSISELLTE LALKTGDPTA ALAAMVAHIA ELVVRLALMA E RTHPGSEI ...String: SGTVTFDITN ISHKAIDIIL KVVLGIAEHE GTEVTFHSER GQLQIEVKNL HEEDKRLIEQ AIEAARLADS PDPESVARAV ELLTKVAKA STNTELIQFI VKELLELARK LTDPKDLAKV LDSISELLTE LALKTGDPTA ALAAMVAHIA ELVVRLALMA E RTHPGSEI VKKAVKLVQE VAEEVLEAAQ LMLEKPNSDE VAKKLEEVAK KAIEACIELQ QILEAWAKER GDQDLLREVR EH KLQILTI AVAYKAAQMG VTVLKHTHGW VVFLVILGLH KQQAEQLLRF VHRVAHALGV TLSITFSGDI VVIAVTVGAS EEE KKEVRK IVKEIAKQLR HAETEEEAKE IVQRVIEEWQ EEGGSG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.971 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: 150 mM NaCl, 40 mM Tris pH 8.0 | |||||||||
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 grids imaged: 1 / Number real images: 4213 / Average exposure time: 5.0 sec. / Average electron dose: 52.0 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 |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Initial model type: in silico model |
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Details | Initial fit was done using Chimera using Rigid body from In silico model. Then Isolde and Namdinator were used. Coot and Phenix were also used. |
Refinement | Protocol: FLEXIBLE FIT |
Output model | PDB-8utm: |