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- EMDB-3853: Cryo-EM structure of human apoferritin H -

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Basic information

Entry
Database: EMDB / ID: EMD-3853
TitleCryo-EM structure of human apoferritin H
Map datahuman apoferritin H
Sample
  • Complex: Human apoferritin H
    • Protein or peptide: Ferritin heavy chain
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDudkina NV / Welsch S
CitationJournal: To Be Published
Title: Falcon 3 Electron Counting detector enables high resolution cryo-EM structures
Authors: Dudkina NV / Welsch S
History
DepositionAug 24, 2017-
Header (metadata) releaseSep 6, 2017-
Map releaseSep 6, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3853.png

Downloads & links

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Map

FileDownload / File: emd_3853.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman apoferritin H
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211.4 Å		1.06 Å/pix.
x 200 pix.
= 211.4 Å		1.06 Å/pix.
x 200 pix.
= 211.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.2
Minimum - Maximum-0.43306845 - 0.70305634
Average (Standard dev.)-0.0000544374 (±0.051229455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0571.0571.057
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z211.400211.400211.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.4330.703-0.000

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Supplemental data

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Additional map: #1

Fileemd_3853_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_3853_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human apoferritin H

EntireName: Human apoferritin H
Components
  • Complex: Human apoferritin H
    • Protein or peptide: Ferritin heavy chain

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Supramolecule #1: Human apoferritin H

SupramoleculeName: Human apoferritin H / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 509 KDa

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MTTASTSQVR QNYHQDSEA A INRQINLE LY ASYVYLS MSY YFDRDD VALK NFAKY FLHQS HEER EHAEKL MKL QNQRGGR IF LQDIKKPD C DDWESGLNA MECALHLEKN VNQSLLELH K LATDKNDP HL CDFIETH YLN EQVKAI KELGDHVTNL RKMG ...String:
MTTASTSQVR QNYHQDSEA A INRQINLE LY ASYVYLS MSY YFDRDD VALK NFAKY FLHQS HEER EHAEKL MKL QNQRGGR IF LQDIKKPD C DDWESGLNA MECALHLEKN VNQSLLELH K LATDKNDP HL CDFIETH YLN EQVKAI KELGDHVTNL RKMG APESG LAEYL FDKH TLGDSD NES

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Formula: PBS
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Protein was applied to glow-discharged Quantifoil R2/2 grids.
DetailsThe protein was provided by Institute of Biophysics of Chinese Academy of Sciences

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 10.0 mrad
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 203 / Average exposure time: 55.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 126194
CTF correctionSoftware: (Name: Gctf (ver. 1.06), RELION (ver. 2.0-beta))
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1v1w

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0-beta) / Number images used: 37000
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.0-beta)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.0-beta)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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