+Open data
-Basic information
Entry | Database: PDB / ID: 8ew2 | ||||||
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Title | Cryo-EM structure of Aldolase embedded in crystalline ice | ||||||
Components | Fructose-bisphosphate aldolase A | ||||||
Keywords | LYASE / Aldolase / Crystalline ice | ||||||
Function / homology | Function and homology information negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Shi, H. / Wu, C. / Zhang, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Structure / Year: 2023 Title: Addressing compressive deformation of proteins embedded in crystalline ice. Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang / Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ew2.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ew2.ent.gz | 207.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ew2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ew2_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ew2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ew2_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 8ew2_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/8ew2 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/8ew2 | HTTPS FTP |
-Related structure data
Related structure data | 28640MC 8bqnC 8ew0C 8f49C 8f7yC 8hhsC 8hi2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39263.672 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00883, fructose-bisphosphate aldolase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Aldolase from rabbit / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.5 / Details: 20 mM HEPES pH 7.5, 50-mM NaCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10300 / Symmetry type: POINT | ||||||||||||||||||||||||
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