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Yorodumi- EMDB-5438: 3D reconstruction of a self-assembling designed oligomer with oct... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5438 | |||||||||
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Title | 3D reconstruction of a self-assembling designed oligomer with octahedral symmetry | |||||||||
Map data | Reconstruction of designed self-assembling protein oligomer with octahedral symmetry | |||||||||
Sample |
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Keywords | octahedral symmetry / designed | |||||||||
Function / homology | Function and homology information propanediol degradation polyhedral organelle / propanediol catabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Salmonella enterica (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Vollmar BS / King NP / Baker D / Gonen T | |||||||||
Citation | Journal: Science / Year: 2012 Title: Computational design of self-assembling protein nanomaterials with atomic level accuracy. Authors: Neil P King / William Sheffler / Michael R Sawaya / Breanna S Vollmar / John P Sumida / Ingemar André / Tamir Gonen / Todd O Yeates / David Baker / Abstract: We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify ...We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials. | |||||||||
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_5438.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-5438-v30.xml emd-5438.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_5438_1.jpg emd_5438_2.tif | 49.5 KB 178.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5438 | HTTPS FTP |
-Validation report
Summary document | emd_5438_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_5438_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_5438_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5438 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5438.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of designed self-assembling protein oligomer with octahedral symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.474 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 : Designed protein oligomer with octahedral symmetry. The model for...
Entire | Name: Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L |
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Components |
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-Supramolecule #1000: Designed protein oligomer with octahedral symmetry. The model for...
Supramolecule | Name: Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L type: sample / ID: 1000 / Details: Monodisperse sample / Oligomeric state: 24 / Number unique components: 1 |
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Molecular weight | Theoretical: 480 KDa |
-Macromolecule #1: Propanediol utilization polyhedral body protein PduT
Macromolecule | Name: Propanediol utilization polyhedral body protein PduT / type: protein_or_peptide / ID: 1 Details: Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L Number of copies: 24 / Recombinant expression: Yes |
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Source (natural) | Organism: Salmonella enterica (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET29b |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8 / Details: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT |
Grid | Details: Quantifoil R1.2/1.3 holey carbon 400 mesh copper grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III Method: Blotted with filter paper and plunged into liquid ethane. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jul 12, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 565 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 217096 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.12 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu). |
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CTF correction | Details: CTFFIND3 |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: FREALIGN Details: Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel. Number images used: 42025 |