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Open data
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Basic information
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Title | A DARPin displayed on a designed tetrahedral protein scaffold | |||||||||
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![]() | scaffold / tetrahedral / darpin / symmetrical / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Suder DS / Gonen S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mitigating the Blurring Effect of CryoEM Averaging on a Flexible and Highly Symmetric Protein Complex through Sub-Particle Reconstruction. Authors: Diana S Suder / Shane Gonen / ![]() Abstract: Many macromolecules are inherently flexible as a feature of their structure and function. During single-particle CryoEM processing, flexible protein regions can be detrimental to high-resolution ...Many macromolecules are inherently flexible as a feature of their structure and function. During single-particle CryoEM processing, flexible protein regions can be detrimental to high-resolution reconstruction as signals from thousands of particles are averaged together. This "blurring" effect can be difficult to overcome and is possibly more pronounced when averaging highly symmetric complexes. Approaches to mitigating flexibility during CryoEM processing are becoming increasingly critical as the technique advances and is applied to more dynamic proteins and complexes. Here, we detail the use of sub-particle averaging and signal subtraction techniques to precisely target and resolve flexible DARPin protein attachments on a designed tetrahedrally symmetric protein scaffold called DARP14. Particles are first aligned as full complexes, and then the symmetry is reduced by alignment and focused refinement of the constituent subunits. The final reconstructions we obtained were vastly improved over the fully symmetric reconstructions, with observable secondary structure and side-chain placement. Additionally, we were also able to reconstruct the core region of the scaffold to 2.7 Å. The data processing protocol outlined here is applicable to other dynamic and symmetric protein complexes, and our improved maps could allow for new structure-guided variant designs of DARP14. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 69.5 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() | 40.7 MB 40.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 754.9 KB | Display | ![]() |
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Full document | ![]() | 754.5 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43167_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43167_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : DARPin with a helical connection to a chain of a designed protein...
Entire | Name: DARPin with a helical connection to a chain of a designed protein scaffold |
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Components |
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-Supramolecule #1: DARPin with a helical connection to a chain of a designed protein...
Supramolecule | Name: DARPin with a helical connection to a chain of a designed protein scaffold type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: DARPin protein scaffold
Macromolecule | Name: DARPin protein scaffold / type: protein_or_peptide / ID: 1 Details: with a helical connection to a chain of a designed protein scaffold Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 32.208723 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KDSPIIEANG TLDELTSFIG EAKHYVDEEM KGILEEIQND IYKIMGEIGS KGKIEGISEE RIAWLLKLIL RYMEMVNLKS FVLPGGTLE SAKLDVCRTI ARRALRKVLT VTREFGIGAE AAAYLLALSD LLFLLARVIE IELGKKLLEA ARAGQDDEVR I LMANGADV ...String: KDSPIIEANG TLDELTSFIG EAKHYVDEEM KGILEEIQND IYKIMGEIGS KGKIEGISEE RIAWLLKLIL RYMEMVNLKS FVLPGGTLE SAKLDVCRTI ARRALRKVLT VTREFGIGAE AAAYLLALSD LLFLLARVIE IELGKKLLEA ARAGQDDEVR I LMANGADV NAHDDQGSTP LHLAAWIGHP EIVEVLLKHG ADVNARDTDG WTPLHLAADN GHLEIVEVLL KYGADVNAQD AY GLTPLHL AADRGHLEIV EVLLKHGADV NAQDKFGKTA FDISIDNGNE DLAEILQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |