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- EMDB-20026: Human apoferritin at 1.75 Angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-20026
TitleHuman apoferritin at 1.75 Angstrom
Map dataHuman Apoferritin
Sample
  • Complex: Human Apoferritin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.75 Å
AuthorsZhang K / Pintilie G / Li S / Chiu W
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesP41GM103832 United States
National Institutes of Health/National Institute of General Medical SciencesS10OD021600 United States
National Institutes of Health/National Institute of General Medical SciencesR01GM079429 United States
CitationJournal: Nat Methods / Year: 2020
Title: Measurement of atom resolvability in cryo-EM maps with Q-scores.
Authors: Grigore Pintilie / Kaiming Zhang / Zhaoming Su / Shanshan Li / Michael F Schmid / Wah Chiu /
Abstract: Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We ...Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.
History
DepositionMar 27, 2019-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateApr 15, 2020-
Current statusApr 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20026.png

Downloads & links

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Map

FileDownload / File: emd_20026.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Apoferritin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 336 pix.
= 218.4 Å		0.65 Å/pix.
x 336 pix.
= 218.4 Å		0.65 Å/pix.
x 336 pix.
= 218.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.060507137 - 0.10878385
Average (Standard dev.)-0.00000039951 (±0.0063883043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 218.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z218.400218.400218.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-0.0610.109-0.000

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Supplemental data

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Additional map: One protomer

Fileemd_20026_additional_1.map
AnnotationOne protomer
Projections & Slices
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Additional map: unmasked map

Fileemd_20026_additional_2.map
Annotationunmasked map
Projections & Slices
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Half map: Half map 1

Fileemd_20026_half_map_1.map
AnnotationHalf map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_20026_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Sample components

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Entire : Human Apoferritin

EntireName: Human Apoferritin
Components
  • Complex: Human Apoferritin

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Supramolecule #1: Human Apoferritin

SupramoleculeName: Human Apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 480 KDa

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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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 1100 / Average exposure time: 6.0 sec. / Average electron dose: 7.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 80000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 70648
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

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