|Entry||Database: EMDB / ID: EMD-30208|
|Title||Cryo-EM reconstruction of E.coli beta-galactosidase (2 mM PEG8)|
|Function / homology|
Function and homology information
beta-galactosidase complex / beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity / carbohydrate binding / magnesium ion binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta-galactosidase, domain 4 / Beta galactosidase small chain/ domain 5 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, active site / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. ...Glycoside hydrolase, family 2, beta-galactosidase / Beta-galactosidase, domain 4 / Beta galactosidase small chain/ domain 5 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, active site / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.2 Å|
|Authors||Zhang Z / Ohto U / Shimizu T|
|Citation||Journal: Structure / Year: 2021|
Title: Improving particle quality in cryo-EM analysis using a PEGylation method.
Authors: Zhikuan Zhang / Hideki Shigematsu / Toshiyuki Shimizu / Umeharu Ohto /
Abstract: Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation ...Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation because it causes severe particle aggregation and/or denaturation. This effect is thought to occur because particles tend to stick to the "deadly" air-water interface during vitrification. Here, we report a method for PEGylation of proteins that can efficiently protect particles against such problems during vitrification. This method alleviates the laborious process of fine-tuning the vitrification conditions, allowing for analysis of samples that would otherwise be discarded.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_30208.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.204 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire : E.coli beta-galactosidase (2 mM PEG8)
|Entire||Name: E.coli beta-galactosidase (2 mM PEG8)|
-Supramolecule #1: E.coli beta-galactosidase (2 mM PEG8)
|Supramolecule||Name: E.coli beta-galactosidase (2 mM PEG8) / type: complex / ID: 1 / Parent: 0|
|Source (natural)||Organism: Escherichia coli (E. coli)|
|Processing||single particle reconstruction|
|Vitrification||Cryogen name: ETHANE|
|Electron beam||Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2|
|Initial angle assignment||Type: RANDOM ASSIGNMENT|
|Final angle assignment||Type: RANDOM ASSIGNMENT|
|Final reconstruction||Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20406|
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