|Entry||Database: EMDB / ID: 5438|
|Title||3D reconstruction of a self-assembling designed oligomer with octahedral symmetry|
|Keywords||octahedral symmetry / designed|
|Sample||Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L|
|Source||Salmonella enterica / bacteria / サルモネラ・エンテリカ, サルモネラ・コレレスイス, ブタコレラ菌|
|Map data||Reconstruction of designed self-assembling protein oligomer with octahedral symmetry|
|Method||single particle reconstruction, at 20 Å resolution|
|Authors||Vollmar BS / King NP / Baker D / Gonen T|
|Citation||Science, 2012, 336, 1171-1174|
|Date||Deposition: Jun 24, 2012 / Header (metadata) release: Jun 29, 2012 / Map release: Jun 29, 2012 / Last update: Jun 24, 2012|
Downloads & links
|File||emd_5438.map.gz (map file in CCP4 format, 6751 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.474 Å|
CCP4 map header:
-Entire Designed protein oligomer with octahedral symmetry. The model for...
|Entire||Name: Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L|
Details: Monodisperse sample / Number of components: 1 / Oligomeric State: 24
|Mass||Theoretical: 480 kDa|
-Component #1: protein, Propanediol utilization polyhedral body protein PduT
|Protein||Name: Propanediol utilization polyhedral body protein PduT|
Details: Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Recombinant expression: Yes / Number of Copies: 24
|Source||Species: Salmonella enterica / bacteria / サルモネラ・エンテリカ, サルモネラ・コレレスイス, ブタコレラ菌|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
|Sample solution||Specimen conc.: 0.3 mg/ml / Buffer solution: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT / pH: 8|
|Support film||Quantifoil R1.2/1.3 holey carbon 400 mesh copper grids|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %|
Method: Blotted with filter paper and plunged into liquid ethane.
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Jul 12, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN|
|Lens||Magnification: 100000 X (nominal), 217096 X (calibrated) / Cs: 2.12 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: TVIPS TEMCAM-F816 (8k x 8k)|
|Image acquisition||Number of digital images: 565|
|Processing||Method: single particle reconstruction / Number of projections: 42025|
Details: Particles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).
Applied symmetry: O (octahedral)
|3D reconstruction||Software: FREALIGN / CTF correction: CTFFIND3|
Details: Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
Resolution: 20 Å / Resolution method: FSC 0.5
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi