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Yorodumi- PDB-6xss: CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xss | ||||||
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Title | CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900 | ||||||
Components | C4_nat_HFuse-7900 | ||||||
Keywords | DE NOVO PROTEIN / helical bundle / helical repeat | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Redler, R.L. / Edman, N.I. / Baker, D. / Ekiert, D. / Bhabha, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Design of multi-scale protein complexes by hierarchical building block fusion. Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una ...Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una Nattermann / Evelyn Tsai / Ayesha Saleem / Cameron M Chow / Damian Ekiert / Gira Bhabha / David Veesler / David Baker / Abstract: A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two ...A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xss.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xss.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xss_validation.pdf.gz | 940.1 KB | Display | wwPDB validaton report |
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Full document | 6xss_full_validation.pdf.gz | 975.1 KB | Display | |
Data in XML | 6xss_validation.xml.gz | 40.5 KB | Display | |
Data in CIF | 6xss_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xss ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xss | HTTPS FTP |
-Related structure data
Related structure data | 22305MC 6xh5C 6xi6C 6xnsC 6xt4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10599 (Title: CryoEM map of designed helical fusion protein C4_nat_HF-7900 Data size: 2.0 TB Data #1: Unaligned multiframe movies of C4_nat_HF-7900 [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 28706.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Lemo21 (DE3) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Designed fusion of helical bundle and helical repeat proteins Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21 Lemo21 (DE3) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 57.05 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144329 / Symmetry type: POINT |