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

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Entry
Database: PDB / ID: 4v1w
Title3D structure of horse spleen apoferritin determined by electron cryomicroscopy
DescriptorFERRITIN LIGHT CHAIN
KeywordsSTORAGE PROTEIN / IRON STORAGE / IRON TRANSPORT / FERRITINS / APOFERRITINS / HORSES / METALS / SPLEEN
Specimen sourceEquus caballus / mammal / HORSE / ウマ /
MethodElectron microscopy (4.7 Å resolution / Particle / Single particle)
AuthorsRusso, C.J. / Passmore, L.A.
CitationScience, 2014, 346, 1377-1380

Science, 2014, 346, 1377-1380 Yorodumi Papers
Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy.
Christopher J Russo / Lori A Passmore

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

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  • Simplified surface model + fitted atomic model
  • EMDB-2788
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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: Polypeptide(L) ...
FERRITIN LIGHT CHAIN / FERRITIN L SUBUNIT


Mass: 19872.428 Da / Num. of mol.: 24 / Source: (natural) Equus caballus / mammal / ウマ / / References: UniProt: P02791

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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 FIELD / 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
IDNameCategoryFitting IDImage processing ID
1REFMACMODEL FITTING1
2RELIONRECONSTRUCTION1
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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