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- EMDB-0025: Influenza hemagglutinin (HA) trimer reconstruction at 3.2 Angstro... -

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Basic information

Entry
Database: EMDB / ID: 0025
TitleInfluenza hemagglutinin (HA) trimer reconstruction at 3.2 Angstrom resolution using data from EMPIAR-10097 processed with Warp and cryoSPARC
Map data
SampleInfluenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2:
SourceInfluenza A virus (A/Hong Kong/1/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsTegunov D / Cramer P
CitationJournal: Biorxiv / Year: 2018
Title: Real-time cryo-EM data pre-processing with Warp
Authors: Tegunov D / Cramer P
DateDeposition: May 22, 2018 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jun 27, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0025.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 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:1.2 (by author), 1.2 (movie #1):
Minimum - Maximum-4.044406 - 6.6609964
Average (Standard dev.)-0.00011054852 (0.16333474)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 335.36 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/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-4.0446.661-0.000

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Supplemental data

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Mask #1

Fileemd_0025_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 A/Hong Kong/1/1968 H3N2

EntireName: Influenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2
Number of components: 2

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Component #1: protein, Influenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2

ProteinName: Influenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2
Recombinant expression: No
MassTheoretical: 150 kDa
SourceSpecies: Influenza A virus (A/Hong Kong/1/1968(H3N2))
Source (engineered)Expression System: Homo sapiens (human) / Strain: HEK293

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Component #2: protein, Influenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2

ProteinName: Influenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2
Recombinant expression: No

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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: Same as EMD-8731 / pH: 7.4
Support filmSame as EMD-8731
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Details: Same as EMD-8731.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Same as EMD-8731
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 82 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500. X (nominal), 38167. 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 acquisition

Image acquisitionNumber of digital images: 847 / Sampling size: 5 microns / Details: Same as EMD-8731

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 249495
3D reconstructionAlgorithm: FOURIER SPACE
CTF correction: On-the-fly correction in cryoSPARC, based on local defocus values from Warp
Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Mask used for FSC automatically generated in cryoSPARC.
FSC plot
(resolution estimation)

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