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- PDB-4v1w: 3D structure of horse spleen apoferritin determined by electron c... -

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Basic information

Entry
Database: PDB / ID: 4v1w
Title3D structure of horse spleen apoferritin determined by electron cryomicroscopy
ComponentsFERRITIN LIGHT CHAIN
KeywordsSTORAGE PROTEIN / IRON STORAGE / IRON TRANSPORT / FERRITINS / APOFERRITINS / HORSES / METALS / SPLEEN
Function / homologyFerritin-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
Specimen sourceEQUUS CABALLUS (horse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.7 Å resolution
AuthorsRusso, C.J. / Passmore, L.A.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Oct 2, 2014 / Release: Dec 10, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 10, 2014Structure modelrepositoryInitial release
1.1Dec 31, 2014Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_image_scans / em_software_em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2788
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERRITIN LIGHT CHAIN
B: FERRITIN LIGHT CHAIN
C: FERRITIN LIGHT CHAIN
D: FERRITIN LIGHT CHAIN
E: FERRITIN LIGHT CHAIN
F: FERRITIN LIGHT CHAIN
G: FERRITIN LIGHT CHAIN
H: FERRITIN LIGHT CHAIN
I: FERRITIN LIGHT CHAIN
J: FERRITIN LIGHT CHAIN
K: FERRITIN LIGHT CHAIN
L: FERRITIN LIGHT CHAIN
M: FERRITIN LIGHT CHAIN
N: FERRITIN LIGHT CHAIN
O: FERRITIN LIGHT CHAIN
P: FERRITIN LIGHT CHAIN
Q: FERRITIN LIGHT CHAIN
R: FERRITIN LIGHT CHAIN
S: FERRITIN LIGHT CHAIN
T: FERRITIN LIGHT CHAIN
U: FERRITIN LIGHT CHAIN
V: FERRITIN LIGHT CHAIN
W: FERRITIN LIGHT CHAIN
X: FERRITIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)476,93824
Polyers476,93824
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein/peptide ...
FERRITIN LIGHT CHAIN / / FERRITIN L SUBUNIT


Mass: 19872.428 Da / Num. of mol.: 24 / Source: (natural) EQUUS CABALLUS (horse) / Tissue: SPLEEN / References: UniProt: P02791

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HORSE SPLEEN APOFERRITIN / Type: COMPLEX
Buffer solutionName: PBS / Details: PBS / pH: 7.4
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: 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
MicroscopyMicroscope model: FEI POLARA 300 / Date: Mar 8, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Calibrated magnification: 104012 / Nominal defocus max: 3639 nm / Nominal defocus min: 1573 nm / Cs: 2 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
CTF correctionDetails: PER PARTICLE
SymmetryPoint symmetry: O
3D reconstructionResolution: 4.7 Å / Number of particles: 483 / Actual pixel size: 1.346
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2788. (DEPOSITION ID: 12832).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY / Ref protocol: FLEXIBLE FIT / Target criteria: Maximum likelihood
Atomic model buildingPDB-ID: 2W0O
Least-squares processHighest resolution: 4.7 Å
Refine hist #LASTHighest resolution: 4.7 Å
Number of atoms included #LASTProtein: 32736 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 32736

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