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- EMDB-22658: Apoferritin structure at 1.36 angstrom resolution determined from... -

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Basic information

Entry
Database: EMDB / ID: EMD-22658
TitleApoferritin structure at 1.36 angstrom resolution determined from a 300 kV Titan Krios G3i electron microscope with Falcon4 detector
Map data
SampleApoferritinFerritin:
Ferritin heavy chain / (ligand) x 3
Function / homology
Function and homology information


intracellular ferritin complex / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / cellular iron ion homeostasis / iron ion transport ...intracellular ferritin complex / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / cellular iron ion homeostasis / iron ion transport / tertiary granule lumen / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / neutrophil degranulation / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Ferritin / Ferritin, conserved site / Ferritin-like / Ferritin-like superfamily / Ferritin-like diiron domain / Ferritin/DPS protein domain
Ferritin heavy chain
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.36 Å
AuthorsZhang K / Pintilie G / Li S / Schmid M / Chiu W
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129564 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: Cell Res / Year: 2020
Title: Resolving individual atoms of protein complex by cryo-electron microscopy.
Authors: Kaiming Zhang / Grigore D Pintilie / Shanshan Li / Michael F Schmid / Wah Chiu /
Validation ReportPDB-ID: 7k3w

SummaryFull reportAbout validation report
History
DepositionSep 14, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateNov 18, 2020-
Current statusNov 18, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7k3w
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k3w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22658.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 330 pix.
= 165.66 Å
0.5 Å/pix.
x 330 pix.
= 165.66 Å
0.5 Å/pix.
x 330 pix.
= 165.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.502 Å
Density
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.17907393 - 0.3772344
Average (Standard dev.)0.00025450144 (±0.019216025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 165.65999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5020.5020.502
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z165.660165.660165.660
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.1790.3770.000

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Supplemental data

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Sample components

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Entire Apoferritin

EntireName: ApoferritinFerritin / Number of components: 5

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Component #1: protein, Apoferritin

ProteinName: ApoferritinFerritin / Recombinant expression: No
MassExperimental: 480 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #2: protein, Ferritin heavy chain

ProteinName: Ferritin heavy chain / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 20.116547 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #3: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 270 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #4: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 112 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

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Component #5: ligand, water

LigandName: water / Number of Copies: 2680 / 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.: 0.2 mg/mL / Buffer solution: 50 mM Tris-HCl (pH 8.0), 150 mM NaCl / pH: 8
VitrificationCryogen name: ETHANE

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 500643
3D reconstructionSoftware: RELION / Resolution: 1.36 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: CC
Input PDB model: 3AJO
Chain ID: A
Output model

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