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- EMDB-8428: Cryo-EM structure of horse spleen apoferritin deposited by micros... -

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Basic information

Entry
Database: EMDB / ID: EMD-8428
TitleCryo-EM structure of horse spleen apoferritin deposited by microsprayer
Map dataApoferritin
Sample
  • Complex: apoferritin from equine spleen
Function / homology
Function and homology information


ferritin complex / autolysosome / : / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / cytoplasmic vesicle / 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: 3.0 Å
AuthorsFu Z / Feng X / Kaledhonkar S / Jia Y / Shah B / Jin A / Liu Z / Sun M / Chen B / Grassucci RA ...Fu Z / Feng X / Kaledhonkar S / Jia Y / Shah B / Jin A / Liu Z / Sun M / Chen B / Grassucci RA / Ren Y / Jiang H / Frank J / Lin Q
Funding support United States, China, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55440 United States
China Scholarship CouncilNo. 201406120114 China
CitationJournal: Structure / Year: 2017
Title: A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM.
Authors: Xiangsong Feng / Ziao Fu / Sandip Kaledhonkar / Yuan Jia / Binita Shah / Amy Jin / Zheng Liu / Ming Sun / Bo Chen / Robert A Grassucci / Yukun Ren / Hongyuan Jiang / Joachim Frank / Qiao Lin /
Abstract: We describe a spraying-plunging method for preparing cryoelectron microscopy (cryo-EM) grids with vitreous ice of controllable, highly consistent thickness using a microfluidic device. The new ...We describe a spraying-plunging method for preparing cryoelectron microscopy (cryo-EM) grids with vitreous ice of controllable, highly consistent thickness using a microfluidic device. The new polydimethylsiloxane (PDMS)-based sprayer was tested with apoferritin. We demonstrate that the structure can be solved to high resolution with this method of sample preparation. Besides replacing the conventional pipetting-blotting-plunging method, one of many potential applications of the new sprayer is in time-resolved cryo-EM, as part of a PDMS-based microfluidic reaction channel to study short-lived intermediates on the timescale of 10-1,000 ms.
History
DepositionOct 6, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseMar 29, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8428.png

Downloads & links

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Map

FileDownload / File: emd_8428.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoferritin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 180 pix.
= 176.58 Å		0.98 Å/pix.
x 180 pix.
= 176.58 Å		0.98 Å/pix.
x 180 pix.
= 176.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.981 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075 / Movie #1: 0.075
Minimum - Maximum-0.14031605 - 0.22132434
Average (Standard dev.)-0.00015829755 (±0.019004228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 176.58 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9810.9810.981
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z176.580176.580176.580
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1400.221-0.000

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Supplemental data

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Sample components

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Entire : apoferritin from equine spleen

EntireName: apoferritin from equine spleen
Components
  • Complex: apoferritin from equine spleen

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Supramolecule #1: apoferritin from equine spleen

SupramoleculeName: apoferritin from equine spleen / type: complex / ID: 1 / Parent: 0
Details: SIGMA A3641. 7 mg/ml in PBS buffer, 0.2 ?m filtered
Source (natural)Organism: Equus caballus (horse)

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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

Concentration7 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v1w

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4300
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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