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- EMDB-4905: 3D structure of horse spleen apoferritin determined using multifu... -

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Basic information

Entry
Database: EMDB / ID: EMD-4905
Title3D structure of horse spleen apoferritin determined using multifunctional graphene supports for electron cryomicroscopy
Map data
SampleApoferritinFerritin:
Ferritin light chain
Function / homology
Function and homology information


intracellular ferritin complex / autolysosome / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / oxidation-reduction process / iron ion binding / identical protein binding / cytoplasm
Ferritin / Ferritin iron-binding regions signature 1. / Ferritin, conserved site / Ferritin-like / Ferritin-like superfamily / Ferritin-like diiron domain / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin iron-binding regions signature 2. / Ferritin-like diiron domain profile.
Ferritin light chain
Biological speciesEquus caballus (horse) / Horse (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsNaydenova K / Peet MJ / Russo CJ
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Multifunctional graphene supports for electron cryomicroscopy.
Authors: Katerina Naydenova / Mathew J Peet / Christopher J Russo /
Abstract: With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In ...With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In practice, the primary barrier to structure determination is the preparation of a frozen specimen suitable for high-resolution imaging. To address this, we present a multifunctional specimen support for cryoEM, comprising large-crystal monolayer graphene suspended across the surface of an ultrastable gold specimen support. Using a low-energy plasma surface modification system, we tune the surface of this support to the specimen by patterning a range of covalent functionalizations across the graphene layer on a single grid. This support design reduces specimen movement during imaging, improves image quality, and allows high-resolution structure determination with a minimum of material and data.
Validation ReportPDB-ID: 6rjh

SummaryFull reportAbout validation report
DateDeposition: Apr 26, 2019 / Header (metadata) release: Jun 5, 2019 / Map release: Jun 5, 2019 / Update: Jun 19, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • 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-6rjh
  • 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_4905.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 340 pix.
= 220.83 Å
0.65 Å/pix.
x 340 pix.
= 220.83 Å
0.65 Å/pix.
x 340 pix.
= 220.83 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6495 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.017431932 - 0.05763059
Average (Standard dev.)-0.000044081196 (±0.0036568928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 220.83 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.64950.64950.6495
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z220.830220.830220.830
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0970.1830.000

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Supplemental data

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Mask #1

Fileemd_4905_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Apoferritin

EntireName: ApoferritinFerritin / Number of components: 2

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Component #1: protein, Apoferritin

ProteinName: ApoferritinFerritin / Recombinant expression: No
SourceSpecies: Equus caballus (horse)

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Component #2: protein, Ferritin light chain

ProteinName: Ferritin light chain / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 19.532113 kDa
SourceSpecies: Horse (horse)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
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: 37 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 41202
3D reconstructionSoftware: RELION / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 4V1W
Output model

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