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- PDB-4v1w: 3D structure of horse spleen apoferritin determined by electron c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v1w | ||||||
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Title | 3D structure of horse spleen apoferritin determined by electron cryomicroscopy | ||||||
![]() | FERRITIN LIGHT CHAIN | ||||||
![]() | STORAGE PROTEIN / IRON STORAGE / IRON TRANSPORT / FERRITINS / APOFERRITINS / HORSES / METALS / SPLEEN | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
![]() | Russo, C.J. / Passmore, L.A. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 782.2 KB | Display | ![]() |
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PDB format | ![]() | 664.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2788MC M: map data used to model this data 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
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Assembly
Deposited unit | ![]()
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: HORSE SPLEEN APOFERRITIN / Type: COMPLEX |
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Buffer solution | Name: PBS / pH: 7.4 / Details: PBS |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Mar 8, 2013 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104012 X / Nominal defocus max: 3639 nm / Nominal defocus min: 1573 nm / Cs: 2 mm |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: PER PARTICLE | ||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||
3D reconstruction | Resolution: 4.7 Å / Num. of particles: 483 / Actual pixel size: 1.346 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2788. (DEPOSITION ID: 12832). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Target criteria: Maximum likelihood / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building | PDB-ID: 2W0O Accession code: 2W0O / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 4.7 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.7 Å
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