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- EMDB-2788: 3D structure of horse spleen apoferritin determined by electron c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2788 | |||||||||
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Title | 3D structure of horse spleen apoferritin determined by electron cryomicroscopy | |||||||||
![]() | Reconstructed density map of horse spleen apoferritin | |||||||||
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![]() | iron storage | |||||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Russo CJ / Passmore LA | |||||||||
![]() | ![]() 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
Images | ![]() | 192.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v1wMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 180.0 Data #1: Raw unprocessed micrograph movies [micrographs - multiframe] Data #2: Final selected particles [picked particles - multiframe - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstructed density map of horse spleen apoferritin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.346 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Horse spleen apoferritin
Entire | Name: Horse spleen apoferritin |
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Components |
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-Supramolecule #1000: Horse spleen apoferritin
Supramolecule | Name: Horse spleen apoferritin / type: sample / ID: 1000 Oligomeric state: 24 subunits combine to form one octahedral complex Number unique components: 1 |
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Molecular weight | Theoretical: 440 KDa |
-Macromolecule #1: FERRITIN LIGHT CHAIN
Macromolecule | Name: FERRITIN LIGHT CHAIN / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Oligomeric state: 24mer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.5 KDa |
Sequence | UniProtKB: Ferritin light chain |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Grid | Details: MRC-LMB all gold grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Mar 8, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 483 |
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-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U / Chain - #21 - Chain ID: V / Chain - #22 - Chain ID: W / Chain - #23 - Chain ID: X |
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Software | Name: RefMac |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-4v1w: |