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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: EMD-0152
TitleRELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer using particles from micrographs tilted at 40 degrees in EMPIAR-10097
Map datapostprocessed map
Sample
  • Complex: Influenza hemagglutinin (HA) trimer
    • Protein or peptide: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2
    • Protein or peptide: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZivanov J / Nakane T / Scheres SHW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1013 United Kingdom
CitationJournal: 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 /
Abstract: We present a strategy for tackling preferred specimen orientation in single-particle cryogenic electron microscopy by employing tilts during data collection. We also describe a tool to quantify the ...We present a strategy for tackling preferred specimen orientation in single-particle cryogenic electron microscopy by employing tilts during data collection. We also describe a tool to quantify the resulting directional resolution using 3D Fourier shell correlation volumes. We applied these methods to determine the structures at near-atomic resolution of the influenza hemagglutinin trimer, which adopts a highly preferred specimen orientation, and of ribosomal biogenesis intermediates, which adopt moderately preferred orientations.
History
DepositionJul 31, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0152.png

Downloads & links

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Map

FileDownload / File: emd_0152.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.078 / Movie #1: 0.078
Minimum - Maximum-0.30286443 - 0.39587775
Average (Standard dev.)5.9126514e-06 (±0.0112498915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 282.96 Å
α=β=γ: 90.0 °

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
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

Histogram

Histogram (log scale)

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Half map: unfiltered half map 1

Fileemd_0152_half_map_1.map
Annotationunfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 2

Fileemd_0152_half_map_2.map
Annotationunfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza hemagglutinin (HA) trimer

EntireName: Influenza hemagglutinin (HA) trimer
Components
  • Complex: Influenza hemagglutinin (HA) trimer
    • Protein or peptide: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2
    • Protein or peptide: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2

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Supramolecule #1: Influenza hemagglutinin (HA) trimer

SupramoleculeName: Influenza hemagglutinin (HA) trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2

MacromoleculeName: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293
SequenceString: ADPGATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCTL IDALLGDPHC DVFQNETWDL FVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG SNACKRGPGS GFFSRLNWLT KSGSTYPVLN V TMPNNDNF ...String:
ADPGATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCTL IDALLGDPHC DVFQNETWDL FVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG SNACKRGPGS GFFSRLNWLT KSGSTYPVLN V TMPNNDNF DKLYIWGVHH PSTNQEQTSL YVQASGRVTV STRRSQQTII PNIGSRPWVR GLSSRISIYW TIVKPGDVLV IN SNGNLIA PRGYFKMRTG KSSIMRSDAP IDTCISECIT PNGSIPNDKP FQNVNKITYG ACPKYVKQNT LKLATGMRNV PEK QTR

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Macromolecule #2: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2

MacromoleculeName: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293
SequenceString:
GLFGAIAGF IENGWEGMID GWYGFRHQNS EGTGQAADLK STQAAIDQIN GKLNRVIEKT NEKFHQIEKE FSEVEGRIQD L EKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTGRQLRE NAEDMGNGCF KIYHKCDNAC IESIRNGTYD HD VYRDEAL NNRFQIK

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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

Concentration0.75 mg/mL
BufferpH: 7.4 / Details: PBS Buffer
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3
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 ...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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38167 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsIn order to account for highly preferred orientations of the specimen, data were acquired using tilts of 40 degrees.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-100 / Average electron dose: 82.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 608919
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4.1.10)For initial estimation
RELION (ver. 3.0)CTF refinement

Details: Standard CTF correction inside RELION's reconstruction.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Details: RELION SGD
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 151596
FSC plot (resolution estimation)

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