+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20907 | |||||||||
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Title | 2.6 Angstrom reconstruction of apo-state streptavidin | |||||||||
Map data | 2.6 Angstrom resolution reconstruction of apo-state streptavidin | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces avidinii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Han Y / Fan X / Yan N | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy. Authors: Yimo Han / Xiao Fan / Haozhe Wang / Fang Zhao / Christopher G Tully / Jing Kong / Nan Yao / Nieng Yan / Abstract: Cryogenic electron microscopy (cryo-EM) has become one of the most powerful techniques to reveal the atomic structures and working mechanisms of biological macromolecules. New designs of the cryo-EM ...Cryogenic electron microscopy (cryo-EM) has become one of the most powerful techniques to reveal the atomic structures and working mechanisms of biological macromolecules. New designs of the cryo-EM grids-aimed at preserving thin, uniform vitrified ice and improving protein adsorption-have been considered a promising approach to achieving higher resolution with the minimal amount of materials and data. Here, we describe a method for preparing graphene cryo-EM grids with up to 99% monolayer graphene coverage that allows for more than 70% grid squares for effective data acquisition with improved image quality and protein density. Using our graphene grids, we have achieved 2.6-Å resolution for streptavidin, with a molecular weight of 52 kDa, from 11,000 particles. Our graphene grids increase the density of examined soluble, membrane, and lipoproteins by at least 5-fold, affording the opportunity for structural investigation of challenging proteins which cannot be produced in large quantity. In addition, our method employs only simple tools that most structural biology laboratories can access. Moreover, this approach supports customized grid designs targeting specific proteins, owing to its broad compatibility with a variety of 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_20907.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-20907-v30.xml emd-20907.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20907_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_20907.png | 153 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20907 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20907 | HTTPS FTP |
-Validation report
Summary document | emd_20907_validation.pdf.gz | 77.9 KB | Display | EMDB validaton report |
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Full document | emd_20907_full_validation.pdf.gz | 77 KB | Display | |
Data in XML | emd_20907_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20907 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20907 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10335 (Title: Apo-state Streptavidin / Data size: 922.4 Data #1: Unaligned 32-frame micrographs of 2.6 angstrom apo-state streptavidin on graphene [micrographs - multiframe] Data #2: Polished particle stacks of 2.6 angstrom apo-state streptavidin on graphene [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20907.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 2.6 Angstrom resolution reconstruction of apo-state streptavidin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.072 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 : Streptavidin
Entire | Name: Streptavidin |
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Components |
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-Supramolecule #1: Streptavidin
Supramolecule | Name: Streptavidin / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Streptomyces avidinii (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.3 nm |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 Blot time 5s. |
Details | NEB N7021S |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 1086 / Average exposure time: 2.4 sec. / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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