|Entry||Database: EMDB / ID: 6801|
|Title||Near-atomic resolution reconstruction of over-focused apoferritin|
|Sample||Near-atomic resolution reconstruction of over-focused apoferritin:|
|Function / homology||Ferritin-like superfamily / Ferritin-like / Ferritin-like diiron domain / Ferritin/DPS protein domain / Ferritin / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile. ...Ferritin-like superfamily / Ferritin-like / Ferritin-like diiron domain / Ferritin/DPS protein domain / Ferritin / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile. / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / Neutrophil degranulation / Iron uptake and transport / iron ion import / autolysosome / intracellular ferritin complex / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / cellular iron ion homeostasis / tertiary granule lumen / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell proliferation / neutrophil degranulation / extracellular exosome / extracellular region / nucleus / cytosol / Ferritin heavy chain|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 3.2 Å resolution|
|Authors||Fan X / Zhao LY|
|Citation||Journal: Structure / Year: 2017|
Title: Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM.
Authors: Xiao Fan / Lingyun Zhao / Chuan Liu / Jin-Can Zhang / Kelong Fan / Xiyun Yan / Hai-Lin Peng / Jianlin Lei / Hong-Wei Wang
Abstract: Volta phase plate (VPP) is a recently developed transmission electron microscope (TEM) apparatus that can significantly enhance the image contrast of biological samples in cryoelectron microscopy, ...Volta phase plate (VPP) is a recently developed transmission electron microscope (TEM) apparatus that can significantly enhance the image contrast of biological samples in cryoelectron microscopy, and therefore provide the possibility to solve structures of relatively small macromolecules at high-resolution. In this work, we performed theoretical analysis and found that using phase plate on objective lens spherical aberration (Cs)-corrected TEM may gain some interesting optical properties, including the over-focus imaging of macromolecules. We subsequently evaluated the imaging strategy of frozen-hydrated apo-ferritin with VPP on a Cs-corrected TEM and obtained the structure of apo-ferritin at near-atomic resolution from both under- and over-focused dataset, illustrating the feasibility and new potential of combining VPP with Cs-corrected TEM for high-resolution cryo-EM.
|Date||Deposition: Jul 21, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6801.map.gz (map file in CCP4 format, 55297 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.88 Å|
CCP4 map header:
-Entire Near-atomic resolution reconstruction of over-focused apoferritin
|Entire||Name: Near-atomic resolution reconstruction of over-focused apoferritin|
Number of components: 1
-Component #1: protein, Near-atomic resolution reconstruction of over-focused ap...
|Protein||Name: Near-atomic resolution reconstruction of over-focused apoferritin|
Recombinant expression: No
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1 mg/ml / pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 0.001 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Sampling size: 14 microns|
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