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- EMDB-2788: 3D structure of horse spleen apoferritin determined by electron c... -

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Basic information

Entry
Database: EMDB / ID: EMD-2788
Title3D structure of horse spleen apoferritin determined by electron cryomicroscopy
Map dataReconstructed density map of horse spleen apoferritin
Sample
  • Sample: Horse spleen apoferritin
  • Protein or peptide: FERRITIN LIGHT CHAIN
Keywordsiron storage
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / 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 light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsRusso CJ / Passmore LA
CitationJournal: Science / Year: 2014
Title: Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy.
Authors: Christopher J Russo / Lori A Passmore /
Abstract: Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they ...Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they cannot be aligned with each other to calculate a three-dimensional density. Much of this movement stems from instabilities in the carbon substrates used to support frozen samples in the microscope. Here we demonstrate a gold specimen support that nearly eliminates substrate motion during irradiation. This increases the subnanometer image contrast such that α helices of individual proteins are resolved. With this improvement, we determine the structure of apoferritin, a smooth octahedral shell of α-helical subunits that is particularly difficult to solve by electron microscopy. This advance in substrate design will enable the solution of currently intractable protein structures.
History
DepositionOct 1, 2014-
Header (metadata) releaseNov 19, 2014-
Map releaseDec 10, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v1w
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2788.png

Downloads & links

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Map

FileDownload / File: emd_2788.map.gz / Format: CCP4 / Size: 8.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstructed density map of horse spleen apoferritin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 132 pix.
= 177.672 Å		1.35 Å/pix.
x 132 pix.
= 177.672 Å		1.35 Å/pix.
x 132 pix.
= 177.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.346 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.47435945 - 0.5409019
Average (Standard dev.)0.00880841 (±0.05253635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions132132132
Spacing132132132
CellA=B=C: 177.672 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3461.3461.346
M x/y/z132132132
origin x/y/z0.0000.0000.000
length x/y/z177.672177.672177.672
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS132132132
D min/max/mean-0.4740.5410.009

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Supplemental data

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Sample components

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Entire : Horse spleen apoferritin

EntireName: Horse spleen apoferritin
Components
  • Sample: Horse spleen apoferritin
  • Protein or peptide: FERRITIN LIGHT CHAIN

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Supramolecule #1000: Horse spleen apoferritin

SupramoleculeName: Horse spleen apoferritin / type: sample / ID: 1000
Oligomeric state: 24 subunits combine to form one octahedral complex
Number unique components: 1
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: FERRITIN LIGHT CHAIN

MacromoleculeName: FERRITIN LIGHT CHAIN / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Oligomeric state: 24mer / Recombinant expression: No
Source (natural)Organism: Equus caballus (horse) / synonym: Horse / Tissue: Spleen
Molecular weightTheoretical: 18.5 KDa
SequenceUniProtKB: Ferritin light chain

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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

Concentration3.5 mg/mL
BufferpH: 7.4 / Details: PBS
GridDetails: MRC-LMB all gold grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
DateMar 8, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 483

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Atomic model buiding 1

Initial modelPDB ID:

2w0o


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U / Chain - #21 - Chain ID: V / Chain - #22 - Chain ID: W / Chain - #23 - Chain ID: X
SoftwareName: RefMac
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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