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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: 2788
Title3D structure of horse spleen apoferritin determined by electron cryomicroscopy
Map dataReconstructed density map of horse spleen apoferritin
SampleHorse spleen apoferritin:
FERRITIN LIGHT CHAIN
Keywordsiron storage
Function / homologyFerritin-like diiron domain / Ferritin iron-binding regions signature 1. / Ferritin / Ferritin/DPS protein domain / Ferritin-like diiron domain profile. / Ferritin-like superfamily / Ferritin-like / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. ...Ferritin-like diiron domain / Ferritin iron-binding regions signature 1. / Ferritin / Ferritin/DPS protein domain / Ferritin-like diiron domain profile. / Ferritin-like superfamily / Ferritin-like / Ferritin, conserved site / Ferritin-like domain / Ferritin iron-binding regions signature 2. / intracellular ferritin complex / intracellular sequestering of iron ion / iron ion transport / ferric iron binding / iron ion binding / cytoplasm / Ferritin light chain
Function and homology information
SourceEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / 4.7 Å resolution
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.
Validation ReportPDB-ID: 4v1w

SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2014 / Header (metadata) release: Nov 19, 2014 / Map release: Dec 10, 2014 / Last update: Feb 17, 2016

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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
  • Download
  • 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

Downloads & links

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Map

Fileemd_2788.map.gz (map file in CCP4 format, 8986 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
132 pix
1.35 Å/pix.
= 177.672 Å
132 pix
1.35 Å/pix.
= 177.672 Å
132 pix
1.35 Å/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
Contour Level:0.16 (by author), 0.16 (movie #1):
Minimum - Maximum-0.47435945 - 0.5409019
Average (Standard dev.)0.00880841 (0.05253635)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions132132132
Origin000
Limit131131131
Spacing132132132
CellA=B=C: 177.672 Å
α=β=γ: 90 deg.

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 / Number of components: 1
Oligomeric State: 24 subunits combine to form one octahedral complex
MassTheoretical: 440 kDa

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Component #1: protein, FERRITIN LIGHT CHAIN

ProteinName: FERRITIN LIGHT CHAIN / Oligomeric Details: 24mer / Recombinant expression: No / Number of Copies: 24
MassTheoretical: 18.5 kDa
SourceSpecies: Equus caballus (horse)
Source (natural)Organ or tissue: Spleen
External referencesUniProt: Ferritin light chain

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.5 mg/ml / Buffer solution: PBS / pH: 7.4
Support filmMRC-LMB all gold grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Mar 8, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Raw dataEMPIAR-10026 (Title: Raw data for the 3D structure of horse spleen apoferritin determined by electron cryomicroscopy
Data size: 180.0 GB
Data #1: Raw unprocessed micrograph movies [micrographs - multiframe]
Data #2: Final selected particles [picked particles - single frame - processed])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 483
3D reconstructionSoftware: RELION / Resolution: 4.7 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Modeling #1Software: RefMac / Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 2W0O
Chain ID: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Output model

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