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- EMDB-0152: RELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0152 | |||||||||
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Title | RELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer using particles from micrographs tilted at 40 degrees in EMPIAR-10097 | |||||||||
![]() | postprocessed map | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Zivanov J / Nakane T / Scheres SHW | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 35.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.7 KB | Display | ![]() |
Images | ![]() | 143.9 KB | ||
Masks | ![]() | 38.4 MB | ![]() | |
Others | ![]() ![]() | 29.7 MB 29.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 419.8 KB | Display | ![]() |
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Full document | ![]() | 418.9 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map 1
File | emd_0152_half_map_1.map | ||||||||||||
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Annotation | unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map 2
File | emd_0152_half_map_2.map | ||||||||||||
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Annotation | unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Influenza hemagglutinin (HA) trimer
Entire | Name: Influenza hemagglutinin (HA) trimer |
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Components |
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-Supramolecule #1: Influenza hemagglutinin (HA) trimer
Supramolecule | Name: Influenza hemagglutinin (HA) trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2
Macromolecule | Name: Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2 type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2
Macromolecule | Name: Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2 type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: GLFGAIAGF IENGWEGMID GWYGFRHQNS EGTGQAADLK STQAAIDQIN GKLNRVIEKT NEKFHQIEKE FSEVEGRIQD L EKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTGRQLRE NAEDMGNGCF KIYHKCDNAC IESIRNGTYD HD VYRDEAL NNRFQIK |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.75 mg/mL |
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Buffer | pH: 7.4 / Details: PBS Buffer |
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Details | In order to account for highly preferred orientations of the specimen, data were acquired using tilts of 40 degrees. |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 38167 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |