[English] 日本語
Yorodumi
- EMDB-33199: Cryo-EM structure of the tubular assembly of WGA protein without ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33199
TitleCryo-EM structure of the tubular assembly of WGA protein without symmetry imposition
Map datacryo-EM map of wheat germ agglutinin protein tube witout symmetry imposition
Sample
  • Complex: Helical complex of wheat germ agglutinin protein with R-SL ligand
Keywordsprotein tube / self-assembly / carbohydrate interaction / PLANT PROTEIN
Biological speciesTriticum aestivum (bread wheat)
Methodhelical reconstruction / cryo EM / Resolution: 15.2 Å
AuthorsZhang L / Chen SY / Liu RY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11774279 China
CitationJournal: ACS Nano / Year: 2023
Title: Evolution of Protein Assemblies Driven by the Switching of Interplay Mode.
Authors: Rongying Liu / Long Li / Shuyu Chen / Zhiwei Yang / Zdravko Kochovski / Shilin Mei / Yan Lu / Lei Zhang / Guosong Chen /
Abstract: A protein assembly with the ability to switch interplay modes of multiple driving forces has been achieved. Although biomolecular systems driven by multiple driving forces have been exploited, work ...A protein assembly with the ability to switch interplay modes of multiple driving forces has been achieved. Although biomolecular systems driven by multiple driving forces have been exploited, work on such a protein assembly capable of switching the interplay modes at nanoscale has been rarely reported so far as a result of their great fabrication challenge. In this work, two sets of driving forces such as ligand-ligand interaction and protein-protein interaction were leveraged to antagonistically underpin the multilayered stackings and trigger the hollow evolution to afford the well-defined hollow rectangular frame of proteins. While these protein frames further collapsed into aggregates, the ligand-ligand interactions were weakened, and the interplay of two sets of driving forces thereby tended to switch into synergistic mode, converting the protein packing mode from porously loose packing to axially dense packing and thus giving rise to a morphological evolution toward a nanosized protein tube. This strategy not only provides a nanoscale understanding on the mechanism underlying the switch of interplay modes in the context of biomacromolecules but also may provide access for diverse sophisticated biomacromolecular nanostructures that are historically inaccessible for conventional self-assembly strategies.
History
DepositionApr 10, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33199.png

Downloads & links

-
Map

FileDownload / File: emd_33199.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of wheat germ agglutinin protein tube witout symmetry imposition
Voxel sizeX=Y=Z: 2.051 Å
Density
Contour LevelBy AUTHOR: 0.034
Minimum - Maximum-0.023304401 - 0.07141643
Average (Standard dev.)0.0032255657 (±0.011686918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 410.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: EM half map of wheat germ agglutinin protein tube

Fileemd_33199_half_map_1.map
AnnotationEM half map of wheat germ agglutinin protein tube
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM half map of wheat germ agglutinin protein tube

Fileemd_33199_half_map_2.map
AnnotationEM half map of wheat germ agglutinin protein tube
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Helical complex of wheat germ agglutinin protein with R-SL ligand

EntireName: Helical complex of wheat germ agglutinin protein with R-SL ligand
Components
  • Complex: Helical complex of wheat germ agglutinin protein with R-SL ligand

-
Supramolecule #1: Helical complex of wheat germ agglutinin protein with R-SL ligand

SupramoleculeName: Helical complex of wheat germ agglutinin protein with R-SL ligand
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Triticum aestivum (bread wheat)

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 6.35 Å
Applied symmetry - Helical parameters - Δ&Phi: 44.55 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 15.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20032
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more