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Yorodumi- EMDB-38083: The SIRM reconstruction of the MC-40 de novo processed HA-trimer -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38083 | |||||||||
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Title | The SIRM reconstruction of the MC-40 de novo processed HA-trimer | |||||||||
Map data | The SIRM reconstruction of the MC-40 de novo processed HA-trimer dataset. | |||||||||
Sample |
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Keywords | Influenza Hemagglutinin Trimer / MEMBRANE PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zhang XZ / Zhu DJ / Cao WL | |||||||||
Funding support | China, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Correction of preferred orientation-induced distortion in cryo-electron microscopy maps. Authors: Dongjie Zhu / Weili Cao / Junxi Li / Chunling Wu / Duanfang Cao / Xinzheng Zhang / Abstract: Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been ...Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to address this preferred orientation problem using tilt-collection strategy and modifications to grids or to air-water interfaces. However, these approaches often require time-consuming experiments, and the effect was always protein dependent. Here, we developed a procedure containing removing misaligned particles and an iterative reconstruction method based on signal-to-noise ratio of Fourier component to correct this distortion by recovering missing data using a purely computational algorithm. This procedure called signal-to-noise ratio iterative reconstruction method (SIRM) was applied on incomplete datasets of various proteins to fix distortion in cryo-EM maps and to a more isotropic resolution. In addition, SIRM provides a better reference map for further reconstruction refinements, resulting in an improved alignment, which ultimately improves map quality and benefits model building. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38083.map.gz | 58.9 MB | EMDB map data format | |
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Header (meta data) | emd-38083-v30.xml emd-38083.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_38083.png | 60.5 KB | ||
Masks | emd_38083_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-38083.cif.gz | 3.9 KB | ||
Others | emd_38083_half_map_1.map.gz emd_38083_half_map_2.map.gz | 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38083 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38083 | HTTPS FTP |
-Validation report
Summary document | emd_38083_validation.pdf.gz | 1018 KB | Display | EMDB validaton report |
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Full document | emd_38083_full_validation.pdf.gz | 1017.5 KB | Display | |
Data in XML | emd_38083_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_38083_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38083 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38083 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The SIRM reconstruction of the MC-40 de novo processed HA-trimer dataset. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38083_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: The conventional reconstructed half map of the MC-40...
File | emd_38083_half_map_1.map | ||||||||||||
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Annotation | The conventional reconstructed half map of the MC-40 de novo processed HA-trimer dataset. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The conventional reconstructed half map of the MC-40...
File | emd_38083_half_map_2.map | ||||||||||||
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Annotation | The conventional reconstructed half map of the MC-40 de novo processed HA-trimer dataset. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza Hemagglutinin Trimer
Entire | Name: Influenza Hemagglutinin Trimer |
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Components |
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-Supramolecule #1: Influenza Hemagglutinin Trimer
Supramolecule | Name: Influenza Hemagglutinin Trimer / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
Details | The micrographs were from EMPIAR-10097 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.0 e/Å2 / Details: Images were from EMPIAR-10097 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.1.2) / Software - details: SIRM-RELION Details: The main map was low-passed to 3.6 Angstrom. The reported resolution was 3.45 Angstrom via FSC-0.143 gold-standard. Number images used: 49634 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2) / Software - details: SIRM-RELION |