7ZFW | pdb_00007zfw

Structure of human 80S ribosome obtained from ssDNA coated grid

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-04-01 Released: 2022-11-23 
  • Deposition Author(s): Hrebik, D., Plevka, P.
  • Funding Organization(s): Grant Agency of the Czech Republic

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules.

Hrebik, D.Gondova, M.Valentova, L.Fuzik, T.Pridal, A.Novacek, J.Plevka, P.

(2022) Acta Crystallogr D Struct Biol 78: 1337-1346

  • DOI: https://doi.org/10.1107/S2059798322009299
  • Primary Citation Related Structures: 
    7ZE1, 7ZFW, 7ZG7

  • PubMed Abstract: 

    Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, the preparation of high-quality samples has become a bottleneck in the cryo-EM structure-determination pipeline. Macromolecules can be damaged during the purification or preparation of vitrified samples for cryo-EM, making them prone to binding to the grid support, to aggregation or to the adoption of preferential orientations at the air-water interface. Here, it is shown that coating cryo-EM grids with a negatively charged polyelectrolyte, such as single-stranded DNA, before applying the sample reduces the aggregation of macromolecules and improves their distribution. The single-stranded DNA-coated grids enabled the determination of high-resolution structures from samples that aggregated on conventional grids. The polyelectrolyte coating reduces the diffusion of macromolecules and thus may limit the negative effects of the contact of macromolecules with the grid support and blotting paper, as well as of the shear forces on macromolecules during grid blotting. Coating grids with polyelectrolytes can readily be employed in any laboratory dealing with cryo-EM sample preparation, since it is fast, simple, inexpensive and does not require specialized equipment.


  • Organizational Affiliation
    • Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 1,222.87 kDa 
  • Atom Count: 13,188 
  • Modeled Residue Count: 615 
  • Deposited Residue Count: 3,774 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (615-MER)A [auth L5]3,774Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Refinement description