6SHT

Molecular structure of mouse apoferritin resolved at 2.7 Angstroms with the Glacios cryo-microscope


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3WNW


Literature

2.7 angstrom cryo-EM structure of vitrified M. musculus H-chain apoferritin from a compact 200 keV cryo-microscope.

Hamdi, F.Tuting, C.Semchonok, D.A.Visscher, K.M.Kyrilis, F.L.Meister, A.Skalidis, I.Schmidt, L.Parthier, C.Stubbs, M.T.Kastritis, P.L.

(2020) PLoS One 15: e0232540-e0232540

  • DOI: https://doi.org/10.1371/journal.pone.0232540
  • Primary Citation of Related Structures:  
    6SHT

  • PubMed Abstract: 

    Here we present the structure of mouse H-chain apoferritin at 2.7 Å (FSC = 0.143) solved by single particle cryogenic electron microscopy (cryo-EM) using a 200 kV device, the Thermo Fisher Glacios®. This is a compact, two-lens illumination system with a constant power objective lens, without any energy filters or aberration correctors, often thought of as a "screening cryo-microscope". Coulomb potential maps reveal clear densities for main chain carbonyl oxygens, residue side chains (including alternative conformations) and bound solvent molecules. We used a quasi-crystallographic reciprocal space approach to fit model coordinates to the experimental cryo-EM map. We argue that the advantages offered by (a) the high electronic and mechanical stability of the microscope, (b) the high emission stability and low beam energy spread of the high brightness Field Emission Gun (X-FEG), (c) direct electron detection technology and (d) particle-based Contrast Transfer Function (CTF) refinement have contributed to achieving high resolution. Overall, we show that basic electron optical settings for automated cryo-electron microscopy imaging can be used to determine structures approaching atomic resolution.


  • Organizational Affiliation

    ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain182Mus musculusMutation(s): 0 
Gene Names: Fth1Fth
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P09528 (Mus musculus)
Explore P09528 
Go to UniProtKB:  P09528
IMPC:  MGI:95588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09528
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.9
RECONSTRUCTIONRELION3.0.5

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Data collection