8RQB

Cryo-EM structure of mouse heavy-chain apoferritin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution.

Kucukoglu, B.Mohammed, I.Guerrero-Ferreira, R.C.Ribet, S.M.Varnavides, G.Leidl, M.L.Lau, K.Nazarov, S.Myasnikov, A.Kube, M.Radecke, J.Sachse, C.Muller-Caspary, K.Ophus, C.Stahlberg, H.

(2024) Nat Commun 15: 8062-8062

  • DOI: https://doi.org/10.1038/s41467-024-52403-5
  • Primary Citation of Related Structures:  
    8RQB

  • PubMed Abstract: 

    Cryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography - a coherent diffractive imaging technique using 4D scanning transmission electron microscopy (4D-STEM) - has recently demonstrated excellent SNR and resolution down to tens of picometers for thin specimens imaged at room temperature. Here we apply 4D-STEM and ptychographic data analysis to frozen hydrated proteins, reaching sub-nanometer resolution 3D reconstructions. We employ low-dose cryo-EM with an aberration-corrected, convergent electron beam to collect 4D-STEM data for our reconstructions. The high frame rate of the electron detector allows us to record large datasets of electron diffraction patterns with substantial overlaps between the interaction volumes of adjacent scan positions, from which the scattering potentials of the samples are iteratively reconstructed. The reconstructed micrographs show strong SNR enabling the reconstruction of the structure of apoferritin protein at up to 5.8 Å resolution. We also show structural analysis of the Phi92 capsid and sheath, tobacco mosaic virus, and bacteriorhodopsin at slightly lower resolutions.


  • Organizational Affiliation

    Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain, N-terminally processed
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
172Mus musculusMutation(s): 0 
Gene Names: Fth1Fth
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth W]
BA [auth B]
BB [auth X]
DA [auth C]
EA [auth D]
AB [auth W],
BA [auth B],
BB [auth X],
DA [auth C],
EA [auth D],
GA [auth E],
HA [auth F],
IA [auth G],
JA [auth H],
LA [auth I],
MA [auth J],
NA [auth K],
OA [auth L],
PA [auth M],
QA [auth N],
SA [auth O],
TA [auth P],
UA [auth Q],
VA [auth R],
WA [auth S],
XA [auth T],
YA [auth U],
Z [auth A],
ZA [auth V]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth C]
FA [auth D]
KA [auth I]
RA [auth O]
AA [auth B],
CA [auth C],
FA [auth D],
KA [auth I],
RA [auth O],
Y [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland200021_200628

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-02
    Changes: Data collection