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- EMDB-7792: Influenza hemagglutinin trimer plunged with a spot-to-plunge time... -

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Basic information

Entry
Database: EMDB / ID: 7792
TitleInfluenza hemagglutinin trimer plunged with a spot-to-plunge time of 100 ms
Map dataCryoSPARC auto-generated full map from the last refinement iteration.
SampleInfluenza hemagglutinin trimer:
SourceInfluenza A virus (A/Hong Kong/26/1983(H3N2))
Methodsingle particle reconstruction / cryo EM / 3.77 Å resolution
AuthorsNoble AJ / Wei H / Dandey VP / Zhang Z / Potter CS / Carragher B
CitationJournal: Nat. Methods / Year: 2018
Title: Reducing effects of particle adsorption to the air-water interface in cryo-EM.
Authors: Alex J Noble / Hui Wei / Venkata P Dandey / Zhening Zhang / Yong Zi Tan / Clinton S Potter / Bridget Carragher
DateDeposition: Apr 15, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.311
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.311
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7792.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
0.85 Å/pix.
= 218.854 Å
256 pix
0.85 Å/pix.
= 218.854 Å
256 pix
0.85 Å/pix.
= 218.854 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8549 Å
Density
Contour Level:0.311 (by author), 0.311 (movie #1):
Minimum - Maximum-0.4929238 - 1.254305
Average (Standard dev.)0.006110061 (0.06405962)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 218.8544 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85489843750.85489843750.8548984375
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z218.854218.854218.854
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.4931.2540.006

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Supplemental data

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Mask #1

Fileemd_7792_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 trimer

EntireName: Influenza hemagglutinin trimer
Details: A/Hong Kong/1/1968 (H3N2), obtained commercially from MyBioSource, catalog MBS434205
Number of components: 1

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Component #1: protein, Influenza hemagglutinin trimer

ProteinName: Influenza hemagglutinin trimer
Details: A/Hong Kong/1/1968 (H3N2), obtained commercially from MyBioSource, catalog MBS434205
Recombinant expression: No
MassExperimental: 150 kDa
SourceSpecies: Influenza A virus (A/Hong Kong/26/1983(H3N2))
Source (engineered)Expression System: unidentified (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: OTHER / Cryogen name: ETHANE
Details: 100 ms spot-to-plunge time. The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 73 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2100.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Raw dataEMPIAR-10175 (Title: Single particle cryoEM of hemagglutinin with spot-to-plunge time of 100ms
Data size: 288.3
Data #1: Full Leginon data collection, including all magnification images and aligned micrographs with and without dose weighting [micrographs - single frame])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 104365
3D reconstructionSoftware: cryoSPARC / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: CryoSPARC SGD

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