[English] 日本語
Yorodumi- EMDB-31256: Cryo-EM structure of designed protein nanoparticle TIP60 (Truncat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31256 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of designed protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins) | ||||||||||||||||||
Map data | Sharpened map by auto-sharpen in Phenix, based on locally-filtered and sharpened map by Relion | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Keywords | Artificial designed protein complex / VIRUS LIKE PARTICLE / DE NOVO PROTEIN | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||
Authors | Obata J / Kawakami N | ||||||||||||||||||
Funding support | Japan, 5 items
| ||||||||||||||||||
Citation | Journal: Angew Chem Int Ed Engl / Year: 2018 Title: Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Authors: Norifumi Kawakami / Hiroki Kondo / Yuki Matsuzawa / Kaoru Hayasaka / Erika Nasu / Kenji Sasahara / Ryoichi Arai / Kenji Miyamoto / Abstract: Protein-based nanoparticles hold promise for a broad range of applications. Here, we report the production of a uniform anionic hollow protein nanoparticle, designated TIP60, which spontaneously ...Protein-based nanoparticles hold promise for a broad range of applications. Here, we report the production of a uniform anionic hollow protein nanoparticle, designated TIP60, which spontaneously assembles from a designed fusion protein subunit based on the geometric features of polyhedra. We show that TIP60 tolerates mutation and both its interior and exterior surfaces can be chemically modified. Moreover, TIP60 forms larger structures upon the addition of a cationic protein. Therefore, TIP60 can be used as a modifiable nano-building block for further molecular assembly. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31256.map.gz | 26.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31256-v30.xml emd-31256.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31256_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_31256.png | 121.1 KB | ||
Masks | emd_31256_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-31256.cif.gz | 6.4 KB | ||
Others | emd_31256_additional_1.map.gz emd_31256_half_map_1.map.gz emd_31256_half_map_2.map.gz | 23 MB 23.1 MB 23.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31256 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31256 | HTTPS FTP |
-Related structure data
Related structure data | 7eq9MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_31256.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map by auto-sharpen in Phenix, based on locally-filtered and sharpened map by Relion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.545 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_31256_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Raw full map
File | emd_31256_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Raw full map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_31256_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_31256_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : 60-meric complex of designed fusion proteins TIP60
Entire | Name: 60-meric complex of designed fusion proteins TIP60 |
---|---|
Components |
|
-Supramolecule #1: 60-meric complex of designed fusion proteins TIP60
Supramolecule | Name: 60-meric complex of designed fusion proteins TIP60 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: 60-meric complex of designed fusion proteins of a pentameric Sm-like protein (3BY7) and a dimeric MyoX-coil domain (2LW9) |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.066 MDa |
-Macromolecule #1: TIP60
Macromolecule | Name: TIP60 / type: protein_or_peptide / ID: 1 Details: Designed fusion protein of pentameric Sm-like protein (3BY7) and dimeric MyoX-coil domain (2LW9) Number of copies: 60 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.794227 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SQDPKNIKIM RLVTGEDIIG NISESQGLIT IKKAFVIIPM QATPGKPVQL VLSPWQPYTD DKEIVIDDSK VITITSPKD DIIKSYESHT RVLENKQVEE ILRLEKEIED LQRMKEQQEL SLTEASLQKL QERRDQELRR LEEE |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 1755 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
| ||||||
---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 205.47 / Target criteria: Correlation coefficient | ||||||
Output model | PDB-7eq9: |