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- EMDB-30206: Cryo-EM reconstruction of E.coli beta-galactosidase (unmodified) -

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Basic information

Entry
Database: EMDB / ID: EMD-30206
TitleCryo-EM reconstruction of E.coli beta-galactosidase (unmodified)
Map data
Sample
  • Complex: E.coli beta-galactosidase (unmodified)
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
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang Z / Ohto U / Shimizu T
CitationJournal: 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.
History
DepositionApr 8, 2020-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.058
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.058
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30206.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 240 pix.
= 288.96 Å
1.2 Å/pix.
x 240 pix.
= 288.96 Å
1.2 Å/pix.
x 240 pix.
= 288.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.204 Å
Density
Contour LevelBy AUTHOR: 0.058 / Movie #1: 0.058
Minimum - Maximum-0.14240435 - 0.23854493
Average (Standard dev.)9.555298e-06 (±0.012148283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 288.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2041.2041.204
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z288.960288.960288.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-250-250-250
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1420.2390.000

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Supplemental data

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Sample components

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Entire : E.coli beta-galactosidase (unmodified)

EntireName: E.coli beta-galactosidase (unmodified)
Components
  • Complex: E.coli beta-galactosidase (unmodified)

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Supramolecule #1: E.coli beta-galactosidase (unmodified)

SupramoleculeName: E.coli beta-galactosidase (unmodified) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9439

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