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- EMDB-30405: Cryo-EM reconstruction of PEGylated tetrameric beta-amylase -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-30405
TitleCryo-EM reconstruction of PEGylated tetrameric beta-amylase
Map data
Sample
  • Complex: Tetrameric beta-amylase
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycoside hydrolase, family 14, conserved site / Glycosyl hydrolase family 14 / Beta-amylase active site 1. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesIpomoea batatas (sweet potato)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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
DepositionJul 26, 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: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.038
  • 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_30405.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 200 pix.
= 166. Å
0.83 Å/pix.
x 200 pix.
= 166. Å
0.83 Å/pix.
x 200 pix.
= 166. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.14075905 - 0.23051265
Average (Standard dev.)2.9370814e-05 (±0.013223947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 166.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z166.000166.000166.000
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/NS200200200
D min/max/mean-0.1410.2310.000

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Supplemental data

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Sample components

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Entire : Tetrameric beta-amylase

EntireName: Tetrameric beta-amylase
Components
  • Complex: Tetrameric beta-amylase

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Supramolecule #1: Tetrameric beta-amylase

SupramoleculeName: Tetrameric beta-amylase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Ipomoea batatas (sweet potato)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244201

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