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Yorodumi- EMDB-0152: RELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer ... -
+Open data
-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 | |||||||||
Map data | postprocessed map | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Zivanov J / Nakane T / Scheres SHW | |||||||||
Funding support | United Kingdom, 1 items
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Citation | 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 / 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0152.map.gz | 35.8 MB | EMDB map data format | |
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Header (meta data) | emd-0152-v30.xml emd-0152.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0152_fsc.xml | 7.7 KB | Display | FSC data file |
Images | emd_0152.png | 143.9 KB | ||
Masks | emd_0152_msk_1.map | 38.4 MB | Mask map | |
Others | emd_0152_half_map_1.map.gz emd_0152_half_map_2.map.gz | 29.7 MB 29.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0152 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0152 | HTTPS FTP |
-Validation report
Summary document | emd_0152_validation.pdf.gz | 419.8 KB | Display | EMDB validaton report |
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Full document | emd_0152_full_validation.pdf.gz | 418.9 KB | Display | |
Data in XML | emd_0152_validation.xml.gz | 13.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0152 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0152 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0152.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
File | emd_0152_msk_1.map | ||||||||||||
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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 |
-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: Homo sapiens (human) |
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: Homo sapiens (human) / Strain: HEK293 |
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: Homo sapiens (human) / Strain: HEK293 |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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.. |
-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: FIELD EMISSION GUN |
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 |