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- EMDB-0152: RELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer ... -

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Basic information

Entry
Database: EMDB / ID: 0152
TitleRELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer using particles from micrographs tilted at 40 degrees in EMPIAR-10097
Map datapostprocessed map
SampleInfluenza hemagglutinin (HA) trimer
  • (Influenza hemagglutinin ...Hemagglutinin (influenza)) x 2
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.10945 Å resolution
AuthorsZivanov J / Nakane T / Scheres SHW
Citation
Journal: Elife / Year: 2018
Title: New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Authors: Jasenko Zivanov / Takanori Nakane / Björn O Forsberg / Dari Kimanius / Wim Jh Hagen / Erik Lindahl / Sjors Hw Scheres
Abstract: Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory ...Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 Å compared to previous RELION versions.
#1: Journal: Nat. Methods / Year: 2017
Title: Addressing preferred specimen orientation in single-particle cryo-EM through tilting.
Authors: Yong Zi Tan / Philip R Baldwin / Joseph H Davis / James R Williamson / Clinton S Potter / Bridget Carragher / Dmitry Lyumkis
DateDeposition: Jul 31, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Dec 26, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.078
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.078
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0152.map.gz (map file in CCP4 format, 40311 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
216 pix
1.31 Å/pix.
= 282.96 Å
216 pix
1.31 Å/pix.
= 282.96 Å
216 pix
1.31 Å/pix.
= 282.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.078 (by author), 0.078 (movie #1):
Minimum - Maximum-0.036682755 - 0.1016331
Average (Standard dev.)0.000005901568 (0.0034351146)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions216216216
Origin0.00.00.0
Limit215.0215.0215.0
Spacing216216216
CellA=B=C: 282.96 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z282.960282.960282.960
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.3030.3960.000

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Supplemental data

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Mask #1

Fileemd_0152_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Influenza hemagglutinin (HA) trimer

EntireName: Influenza hemagglutinin (HA) trimer / Number of components: 3

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Component #1: protein, Influenza hemagglutinin (HA) trimer

ProteinName: Influenza hemagglutinin (HA) trimer / Recombinant expression: No
MassTheoretical: 150 kDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2

ProteinName: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2
Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HEK293

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Component #3: protein, Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2

ProteinName: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2
Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HEK293

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.75 mg/ml / Buffer solution: PBS Buffer / pH: 7.4
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %
Details: 3 microliters of 0.75 mg/mL sample was added to a plasma-cleaned (Gatan Solarus) 1.2-micron-hole, 1.3-micron-spacing holey gold grid (made in-house) and plunge-frozen in liquid ethane using the Cryoplunge 3 system (Gatan) operating at 80% humidity, 298K ambient temperature..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: In order to account for highly preferred orientations of the specimen, data were acquired using tilts of 40 degrees.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 82 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal), 38167.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 151596
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: Standard CTF correction inside RELION's reconstruction.
Resolution: 3.10945 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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