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- EMDB-9277: Single particle cryoEM structure of a DARPin-aldolase platform in... -
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Open data
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Basic information
Entry | Database: EMDB / ID: 9277 |
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Title | Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP |
![]() | DARPin-aldolase platform in complex with GFP, Relion Post processed map with B factor -25 angstrom squared |
![]() | DARPin-aldolase platform in complex with GFP
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Source | synthetic construct (others) / ![]() ![]() ![]() ![]() ![]() |
Method | ![]() ![]() |
![]() | Weaver SJ / Yao Q |
![]() | Journal: Biorxiv / Year: 2018 Title: Fusion of DARPin to aldolase enables visualization of small protein by cryoEM ![]() |
Validation Report | PDB-ID: 6mwq![]() ![]() ![]() |
Date | Deposition: Oct 30, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
![]() | ![]() |
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Header (meta data in XML format) | ![]() ![]() ![]() |
FSC (resolution estimation) | ![]() |
Images | ![]() |
Others | ![]() ![]() |
FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9277 |
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Links
-Related structure data
Related structure data | ![]() M6mwq M: atomic model generated by this map |
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Similar-shape strucutres |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8315 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire DARPin-aldolase platform in complex with GFP
+Component #1: protein, DARPin-aldolase platform in complex with GFP
+Component #2: protein, DARPin, Muscle-type aldolase chimeric fusion
+Component #3: protein, Green fluorescent protein
+Component #4: protein, DARPin, Muscle-type aldolase chimeric fusion
+Component #5: protein, Green fluorescent protein
-Experimental details
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Sample preparation
Specimen | Specimen state: particle / Method: ![]() |
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Sample solution | Specimen conc.: 2.5 mg/ml / pH: 8 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 95 % Details: Grids were frozen on a manual plunger at the Scripps Research Institute Core Microscopy Facility in a 4 degrees C cold room humidified to >95%.. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 165000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
-Image acquisition
Image acquisition #1 | Number of digital images: 1133 Details: All three microscope sessions used grids frozen in the same session. In the first microscopy session the stage was untilted (0 degrees). |
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Image acquisition #2 | Number of digital images: 548 Details: All three microscope sessions used grids frozen in the same session. In the second microscopy session the stage was untilted (0 degrees). |
Image acquisition #3 | Number of digital images: 1180 Details: All three microscope sessions used grids frozen in the same session. In the third microscopy session the stage was tilted to 26 degrees. |
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Image processing
-Atomic model buiding
Modeling #1 | Refinement protocol: rigid body Details: PDB models 5vy5 and 5ma6 were used as starting points. These models were mutated to match the sequence of the DARPin-aldolase platform in complex with GFP that were used. The PDB models were docked into the cryoEM density using Chimera fit into map function. No model refinement was used. Input PDB model: 5VY5, 5MA6, 5MA6 Chain ID: A, A, B |
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Output model |