|Entry||Database: EMDB / ID: 2788|
|Title||3D structure of horse spleen apoferritin determined by electron cryomicroscopy|
|Map data||Reconstructed density map of horse spleen apoferritin|
|Sample||Horse spleen apoferritin:|
FERRITIN LIGHT CHAIN
|Function / homology||Ferritin-like diiron domain / Ferritin iron-binding regions signature 1. / Ferritin / Ferritin/DPS protein domain / Ferritin-like diiron domain profile. / Ferritin-like superfamily / Ferritin-like / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. ...Ferritin-like diiron domain / Ferritin iron-binding regions signature 1. / Ferritin / Ferritin/DPS protein domain / Ferritin-like diiron domain profile. / Ferritin-like superfamily / Ferritin-like / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. / intracellular ferritin complex / intracellular sequestering of iron ion / iron ion transport / ferric iron binding / iron ion binding / cytoplasm / Ferritin light chain|
Function and homology information
|Source||Equus caballus (horse)|
|Method||single particle reconstruction / cryo EM / 4.7 Å resolution|
|Authors||Russo CJ / Passmore LA|
|Citation||Journal: Science / Year: 2014|
Title: Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy.
Authors: Christopher J Russo / Lori A Passmore
Abstract: Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they ...Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they cannot be aligned with each other to calculate a three-dimensional density. Much of this movement stems from instabilities in the carbon substrates used to support frozen samples in the microscope. Here we demonstrate a gold specimen support that nearly eliminates substrate motion during irradiation. This increases the subnanometer image contrast such that α helices of individual proteins are resolved. With this improvement, we determine the structure of apoferritin, a smooth octahedral shell of α-helical subunits that is particularly difficult to solve by electron microscopy. This advance in substrate design will enable the solution of currently intractable protein structures.
|Validation Report||PDB-ID: 4v1w|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 1, 2014 / Header (metadata) release: Nov 19, 2014 / Map release: Dec 10, 2014 / Last update: Feb 17, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_2788.map.gz (map file in CCP4 format, 8986 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.346 Å|
CCP4 map header:
-Entire Horse spleen apoferritin
|Entire||Name: Horse spleen apoferritin / Number of components: 1|
Oligomeric State: 24 subunits combine to form one octahedral complex
|Mass||Theoretical: 440 kDa|
-Component #1: protein, FERRITIN LIGHT CHAIN
|Protein||Name: FERRITIN LIGHT CHAIN / Oligomeric Details: 24mer / Recombinant expression: No / Number of Copies: 24|
|Mass||Theoretical: 18.5 kDa|
|Source||Species: Equus caballus (horse)|
|Source (natural)||Organ or tissue: Spleen|
|External references||UniProt: Ferritin light chain|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 3.5 mg/ml / Buffer solution: PBS / pH: 7.4|
|Support film||MRC-LMB all gold grid|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Mar 8, 2013|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Raw data||EMPIAR-10026 (Title: Raw data for the 3D structure of horse spleen apoferritin determined by electron cryomicroscopy|
Data size: 180.0 GB
Data #1: Raw unprocessed micrograph movies [micrographs - multiframe]
Data #2: Final selected particles [picked particles - single frame - processed])
|Processing||Method: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 483|
|3D reconstruction||Software: RELION / Resolution: 4.7 Å / Resolution method: FSC 0.143, gold-standard|
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