8EMQ

Mouse apoferritin heavy chain with zinc determined using single-particle cryo-EM with Apollo camera.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.66 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


Literature

Characterizing the resolution and throughput of the Apollo direct electron detector.

Peng, R.Fu, X.Mendez, J.H.Randolph, P.S.Bammes, B.E.Stagg, S.M.

(2023) J Struct Biol X 7: 100080-100080

  • DOI: https://doi.org/10.1016/j.yjsbx.2022.100080
  • Primary Citation of Related Structures:  
    8EHG, 8EMQ, 8EN7

  • PubMed Abstract: 

    Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.


  • Organizational Affiliation

    Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States.


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 (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth W]
BA [auth C]
BB [auth X]
CA [auth D]
AA [auth B],
AB [auth W],
BA [auth C],
BB [auth X],
CA [auth D],
EA [auth E],
FA [auth F],
GA [auth G],
IA [auth H],
KA [auth I],
MA [auth J],
NA [auth K],
OA [auth L],
PA [auth M],
QA [auth N],
RA [auth O],
SA [auth P],
TA [auth Q],
UA [auth R],
WA [auth S],
XA [auth T],
Y [auth A],
YA [auth U],
ZA [auth V]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
DA [auth E]
HA [auth G]
JA [auth I]
LA [auth J]
VA [auth R]
DA [auth E],
HA [auth G],
JA [auth I],
LA [auth J],
VA [auth R],
Z [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143805
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM139616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119032

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references