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- EMDB-10101: Apoferritin from mouse at 1.84 angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-10101
TitleApoferritin from mouse at 1.84 angstrom resolutionFerritin
Map dataFerritin
SampleOctahedral complex of 24 apoferritin chains:
Ferritin heavy chain / (ligand) x 3
Function / homology
Function and homology information


Golgi Associated Vesicle Biogenesis / Neutrophil degranulation / Iron uptake and transport / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / ferric iron binding ...Golgi Associated Vesicle Biogenesis / Neutrophil degranulation / Iron uptake and transport / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / ferric iron binding / ferrous iron binding / iron ion transport / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / cytoplasm
Ferritin/DPS protein domain / Ferritin iron-binding regions signature 2. / Ferritin / Ferritin-like superfamily / Ferritin-like / Ferritin, conserved site / Ferritin-like diiron domain / Ferritin-like domain / Ferritin iron-binding regions signature 1. / Ferritin-like diiron domain profile.
Ferritin heavy chain
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.84 Å
AuthorsMills DJ / Pfeil-Gardiner O / Vonck J
CitationJournal: To Be Published
Title: To be published later
Authors: Vonck J / Mills DJ / Pfeil-Gardiner O
Validation ReportPDB-ID: 6s61

SummaryFull reportAbout validation report
DateDeposition: Jul 2, 2019 / Header (metadata) release: Jul 10, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6s61
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10101.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 300 pix.
= 196.8 Å
0.66 Å/pix.
x 300 pix.
= 196.8 Å
0.66 Å/pix.
x 300 pix.
= 196.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.014236959 - 0.05048638
Average (Standard dev.)-0.000074461124 (±0.0039507938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 196.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6560.6560.656
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z196.800196.800196.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1860.303-0.000

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Supplemental data

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Sample components

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Entire Octahedral complex of 24 apoferritin chains

EntireName: Octahedral complex of 24 apoferritin chains / Number of components: 5

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Component #1: protein, Octahedral complex of 24 apoferritin chains

ProteinName: Octahedral complex of 24 apoferritin chains / Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Ferritin heavy chain

ProteinName: Ferritin heavy chain / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 21.097631 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: ligand, FE (III) ION

LigandName: FE (III) ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 5.584505 MDa

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Component #4: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #5: ligand, water

LigandName: water / Number of Copies: 3854 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 120000.0 X (nominal), 182927.0 X (calibrated)
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 1500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1788
Details: Some images were discarding after motion correction (MotionCor2) and ctf estimation (CTFfind4), leaving 1745 for processing.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 441902
3D reconstructionSoftware: RELION / Resolution: 1.84 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL / Details: phenix.real-space-refine
Input PDB model: 2CIH
Output model

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