[English] 日本語
Yorodumi- EMDB-30095: 3.6A beta-galactosidase using JEM-2100F + K2 Summit, SerialEM acq... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30095 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 3.6A beta-galactosidase using JEM-2100F + K2 Summit, SerialEM acquisition, RELION 3.0 processing. | |||||||||
Map data | 3.6A beta-galactosidase, JEM-2100F K2 Summit, SerialEM, RELION 3.0, full map. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Burton-Smith RN / Kayama Y / Song C / Kato T / Murata K | |||||||||
Citation | Journal: Sci Rep / Year: 2021 Title: Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder. Authors: Yoko Kayama / Raymond N Burton-Smith / Chihong Song / Naoya Terahara / Takayuki Kato / Kazuyoshi Murata / Abstract: Recently, the structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method. Many results of cryo-EM SPA ...Recently, the structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method. Many results of cryo-EM SPA are based on data acquired on state-of-the-art cryo-electron microscopes customized for SPA. These are currently only available in limited locations around the world, where securing machine time is highly competitive. One potential solution for this time-competitive situation is to reuse existing multi-purpose equipment, although this comes with performance limitations. Here, a multi-purpose TEM with a side entry cryo-holder was used to evaluate the potential of high-resolution SPA, resulting in a 3 Å resolution map of apoferritin with local resolution extending to 2.6 Å. This map clearly showed two positions of an aromatic side chain. Further, examination of optimal imaging conditions depending on two different multi-purpose electron microscope and camera combinations was carried out, demonstrating that higher magnifications are not always necessary or desirable. Since automation is effectively a requirement for large-scale data collection, and augmenting the multi-purpose equipment is possible, we expanded testing by acquiring data with SerialEM using a β-galactosidase test sample. This study demonstrates the possibilities of more widely available and established electron microscopes, and their applications for cryo-EM SPA. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30095.map.gz | 202.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30095-v30.xml emd-30095.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30095_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_30095.png | 72.5 KB | ||
Masks | emd_30095_msk_1.map | 216 MB | Mask map | |
Others | emd_30095_additional_1.map.gz emd_30095_half_map_1.map.gz emd_30095_half_map_2.map.gz | 97.3 MB 169.3 MB 169.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30095 | HTTPS FTP |
-Validation report
Summary document | emd_30095_validation.pdf.gz | 568.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30095_full_validation.pdf.gz | 567.8 KB | Display | |
Data in XML | emd_30095_validation.xml.gz | 19.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30095 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_30095.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3.6A beta-galactosidase, JEM-2100F K2 Summit, SerialEM, RELION 3.0, full map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_30095_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Local resolution estimated by blocres module of Bsoft.
File | emd_30095_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Local resolution estimated by blocres module of Bsoft. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: 3.6A beta-galactosidase, JEM-2100F K2 Summit, SerialEM, RELION 3.0,...
File | emd_30095_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3.6A beta-galactosidase, JEM-2100F K2 Summit, SerialEM, RELION 3.0, half map 1. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: 3.6A beta-galactosidase, JEM-2100F K2 Summit, SerialEM, RELION 3.0,...
File | emd_30095_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3.6A beta-galactosidase, JEM-2100F K2 Summit, SerialEM, RELION 3.0, half map 2. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : beta-Galactosidase
Entire | Name: beta-Galactosidase |
---|---|
Components |
|
-Supramolecule #1: beta-Galactosidase
Supramolecule | Name: beta-Galactosidase / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 465 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL 2100F |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 5.0 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |