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- EMDB-3651: Cryo-EM asymmetric reconstruction of haemoglobin at 3.6 A determi... -

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Basic information

Entry
Database: EMDB / ID: EMD-3651
TitleCryo-EM asymmetric reconstruction of haemoglobin at 3.6 A determined with the Volta phase plate (subset of particles)
Map dataPostprocessed asymmetric masked map of haemoglobin dataset with 76150 particles
Sample
  • Complex: Hemoglobin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKhoshouei M / Radjainia M / Baumeister W / Danev R
CitationJournal: Nat Commun / Year: 2017
Title: Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate.
Authors: Maryam Khoshouei / Mazdak Radjainia / Wolfgang Baumeister / Radostin Danev /
Abstract: With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with ...With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with the intrinsically low contrast and beam-induced motion of radiation-sensitive organic materials embedded in amorphous ice, and hence they have enabled the structure determination of many macromolecular assemblies to atomic or near-atomic resolution. Nevertheless, there are still limitations and one of them is the size of the target structure. Here, we report the use of a Volta phase plate in determining the structure of human haemoglobin (64 kDa) at 3.2 Å. Our results demonstrate that this method can be applied to complexes that are significantly smaller than those previously studied by conventional defocus-based approaches. Cryo-EM is now close to becoming a fast and cost-effective alternative to crystallography for high-resolution protein structure determination.
History
DepositionMar 24, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateJul 19, 2017-
Current statusJul 19, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0701
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0701
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3651.png

Downloads & links

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Map

FileDownload / File: emd_3651.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed asymmetric masked map of haemoglobin dataset with 76150 particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 100 pix.
= 105. Å		1.05 Å/pix.
x 100 pix.
= 105. Å		1.05 Å/pix.
x 100 pix.
= 105. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0701 / Movie #1: 0.0701
Minimum - Maximum-0.21832137 - 0.34083924
Average (Standard dev.)0.0015186996 (±0.020368665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 104.99999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z105.000105.000105.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.2180.3410.002

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Supplemental data

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Half map: Half1 map from haemoglobin dataset with 76150 particles

Fileemd_3651_half_map_1.map
AnnotationHalf1 map from haemoglobin dataset with 76150 particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2 map from haemoglobin dataset with 76150 particles

Fileemd_3651_half_map_2.map
AnnotationHalf2 map from haemoglobin dataset with 76150 particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hemoglobin

EntireName: Hemoglobin
Components
  • Complex: Hemoglobin

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Supramolecule #1: Hemoglobin

SupramoleculeName: Hemoglobin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE / 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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76150
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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