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Yorodumi- EMDB-22305: CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22305 | |||||||||
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Title | CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | helical bundle / helical repeat / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Redler RL / Edman NI | |||||||||
Funding support | United States, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22305.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-22305-v30.xml emd-22305.xml | 11 KB 11 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22305_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_22305.png | 11 KB | ||
Filedesc metadata | emd-22305.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22305 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22305 | HTTPS FTP |
-Validation report
Summary document | emd_22305_validation.pdf.gz | 595.2 KB | Display | EMDB validaton report |
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Full document | emd_22305_full_validation.pdf.gz | 594.8 KB | Display | |
Data in XML | emd_22305_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_22305_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22305 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22305 | HTTPS FTP |
-Related structure data
Related structure data | 6xssMC 6xh5C 6xi6C 6xnsC 6xt4C C: citing same article (ref.) M: atomic model generated by this map |
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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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22305.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.859 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 fusion of helical bundle and helical repeat proteins
Entire | Name: Designed fusion of helical bundle and helical repeat proteins |
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Components |
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-Supramolecule #1: Designed fusion of helical bundle and helical repeat proteins
Supramolecule | Name: Designed fusion of helical bundle and helical repeat proteins type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: C4_nat_HFuse-7900
Macromolecule | Name: C4_nat_HFuse-7900 / 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: 28.706484 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: ASSWVMLGLL LSLLNRLSLA AEAYKKAIEL DPNDALAWLL LGSVLLLLGR EEEAEEAARK AIELKPEMDS ARRLEGIIEL IRRAREAAE RAQEAAERTG DPRVRELARE LKRLAQEAAE EVRRDPDSKD VNEALKLIVE AIEAAVRALE AAERTGDPEV R ELARELVR ...String: ASSWVMLGLL LSLLNRLSLA AEAYKKAIEL DPNDALAWLL LGSVLLLLGR EEEAEEAARK AIELKPEMDS ARRLEGIIEL IRRAREAAE RAQEAAERTG DPRVRELARE LKRLAQEAAE EVRRDPDSKD VNEALKLIVE AIEAAVRALE AAERTGDPEV R ELARELVR LAVEAAEEVQ RNPSSSDVNE ALKLIVEAID AAVRALEAAE KTGDPEVREL ARELVRLAVE AAEEVQRNPS SE EVNEALK DIVKAIQEAV ESL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.05 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |