[English] 日本語
Yorodumi- EMDB-40055: Focused map of Pex region of Trypanosoma docking complex, (MDH)4-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40055 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Focused map of Pex region of Trypanosoma docking complex, (MDH)4-(Pex5)1-(Pex14)1 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Peroxisomal transport / Import / PEX / TRANSPORT PROTEIN | |||||||||
Biological species | Trypanosoma cruzi strain CL Brener (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Sonani RR / Artur B / Jemiola-Rzeminska M / Lipinski O / Patel SN / Sood T / Dubin G | |||||||||
Funding support | Poland, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Structure of Trypanosoma MDH4-Pex5, close conformation Authors: Sonani RR / Dubin G | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_40055.map.gz | 203.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-40055-v30.xml emd-40055.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40055_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_40055.png | 56.2 KB | ||
Masks | emd_40055_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-40055.cif.gz | 4 KB | ||
Others | emd_40055_half_map_1.map.gz emd_40055_half_map_2.map.gz | 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40055 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40055 | HTTPS FTP |
-Validation report
Summary document | emd_40055_validation.pdf.gz | 939.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_40055_full_validation.pdf.gz | 939.1 KB | Display | |
Data in XML | emd_40055_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_40055_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40055 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40055 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_40055.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_40055_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_40055_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_40055_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of MDH-tetramer and PEX5
Entire | Name: Complex of MDH-tetramer and PEX5 |
---|---|
Components |
|
-Supramolecule #1: Complex of MDH-tetramer and PEX5
Supramolecule | Name: Complex of MDH-tetramer and PEX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Trypanosoma cruzi strain CL Brener (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.25 e/Å2 |
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: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |