+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9021 | |||||||||
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Title | DHF119 filament | |||||||||
Map data | DHF119 filament | |||||||||
Sample |
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Keywords | Protein design / filament / PROTEIN FIBRIL | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Lynch EM / Shen H | |||||||||
Citation | Journal: Science / Year: 2018 Title: De novo design of self-assembling helical protein filaments. Authors: Hao Shen / Jorge A Fallas / Eric Lynch / William Sheffler / Bradley Parry / Nicholas Jannetty / Justin Decarreau / Michael Wagenbach / Juan Jesus Vicente / Jiajun Chen / Lei Wang / Quinton ...Authors: Hao Shen / Jorge A Fallas / Eric Lynch / William Sheffler / Bradley Parry / Nicholas Jannetty / Justin Decarreau / Michael Wagenbach / Juan Jesus Vicente / Jiajun Chen / Lei Wang / Quinton Dowling / Gustav Oberdorfer / Lance Stewart / Linda Wordeman / James De Yoreo / Christine Jacobs-Wagner / Justin Kollman / David Baker / Abstract: We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale ...We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo-electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials. | |||||||||
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_9021.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-9021-v30.xml emd-9021.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_9021.png | 312.5 KB | ||
Filedesc metadata | emd-9021.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9021 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9021 | HTTPS FTP |
-Validation report
Summary document | emd_9021_validation.pdf.gz | 432.5 KB | Display | EMDB validaton report |
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Full document | emd_9021_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | emd_9021_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_9021_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9021 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9021 | HTTPS FTP |
-Related structure data
Related structure data | 6e9zMC 9016C 9017C 9018C 9019C 9020C 6e9rC 6e9tC 6e9vC 6e9xC 6e9yC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_9021.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | DHF119 filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : DHF119 filament
Entire | Name: DHF119 filament |
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Components |
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-Supramolecule #1: DHF119 filament
Supramolecule | Name: DHF119 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: DHF119 filament
Macromolecule | Name: DHF119 filament / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 25.120242 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PEDELKRVEK LVKEAEALLI VAKIKGSKRD LEKALRTAEE AAREAVKVLV QALLEGDPEV ALRAVELVVR VAELLLRIAK ESGSREALL RALIVAEEAA KLAKMVLELA EKQGDPEVAL RAVELVVRVA ELLLRIAKES GSEEALERAL RVAEEAARLA K RVLELAEE ...String: PEDELKRVEK LVKEAEALLI VAKIKGSKRD LEKALRTAEE AAREAVKVLV QALLEGDPEV ALRAVELVVR VAELLLRIAK ESGSREALL RALIVAEEAA KLAKMVLELA EKQGDPEVAL RAVELVVRVA ELLLRIAKES GSEEALERAL RVAEEAARLA K RVLELAEE QGDPLVAKMA VELVKRVAEL LERIARESGS EEAKERAERV REEARELQER VKELRER |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 14.3312 Å Applied symmetry - Helical parameters - Δ&Phi: 43.5023 ° Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 63067 |
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Startup model | Type of model: OTHER / Details: Cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6e9z: |