|Entry||Database: EMDB / ID: 6037|
|Title||Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions|
|Map data||Reconstruction of bacteriophage T7 mature capsid with icosahedral symmetry averaging|
|Sample||Bacteriophage T7 mature phage capsid:|
|Keywords||Bacteriophage T7 / Maturation / DNA packaging / Procapsid / Non-covalent topological linking / Single particle cryo-EM|
|Function / homology||Capsid Gp10A/Gp10B / viral capsid / identical protein binding / Major capsid protein|
Function and homology information
|Source||Enterobacteria phage T7 (bacteriophage)|
|Method||single particle reconstruction / cryo EM / 3.6 Å resolution|
|Authors||Guo F / Liu Z / Fang PA / Zhang Q / Wright ET / Wu W / Zhang C / Vago F / Ren Y / Jakata J / Chiu W / Serwer P / Jiang W|
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014|
Title: Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions.
Authors: Fei Guo / Zheng Liu / Ping-An Fang / Qinfen Zhang / Elena T Wright / Weimin Wu / Ci Zhang / Frank Vago / Yue Ren / Joanita Jakana / Wah Chiu / Philip Serwer / Wen Jiang
|Validation Report||PDB-ID: 3j7x|
SummaryFull reportAbout validation report
|Date||Deposition: Aug 12, 2014 / Header (metadata) release: Sep 24, 2014 / Map release: Oct 15, 2014 / Last update: Nov 19, 2014|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6037.map.gz (map file in CCP4 format, 2000001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.1 Å|
CCP4 map header:
-Entire Bacteriophage T7 mature phage capsid
|Entire||Name: Bacteriophage T7 mature phage capsid / Number of components: 1|
Oligomeric State: 415 copies of gp10A form T=7 icosahedral shell
|Mass||Theoretical: 15.1 MDa|
-Component #1: virus, Enterobacteria phage T7
|Virus||Name: Enterobacteria phage T7 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES|
|Mass||Theoretical: 15.1 MDa|
|Species||Species: Enterobacteria phage T7 (bacteriophage)|
|Source (natural)||Host Species: Escherichia coli (E. coli) / Host category: BACTERIA(EUBACTERIA)|
|Shell #1||Name of element: mature phage capsid / Diameter: 564 Å / T number(triangulation number): 7|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 200 mM NaCl, 10 mM Tris-HCl, 1 mM MgCl2 / pH: 7.4|
|Support film||400 mesh copper grid with one lacy carbon layer|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 90 %|
Method: Blot for 2 seconds twice with 2 mm offset before plunging.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Aug 9, 2010|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal), 57727 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2400 nm|
|Specimen Holder||Holder: Liquid nitrogen-cooled / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 95 K ( 80 - 100 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 364 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / OD range: 1|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 33952|
Details: Particles were selected from scanned micrograph images, first automatically by the ethan method and then by manual screening with the boxer program in EMAN. The TEM instrument contrast transfer function parameters were determined automatically using fitctf2.py and were then visually validated using the EMAN ctfit program. The datasets were then divided into two subsets (even and odd) and processed completely independently, including both initial models and refinements. For 3D reconstructions, the whole datasets were divided into even-odd halves and the initial de novo models and subsequent iterative refinements were all independently performed for each half dataset. The images were first binned 4x to obtain initial models and particle parameters assuming icosahedral symmetry. De novo initial models were built using the random model approach. Random subsets of particles were assigned random initial orientations and iteratively refined until convergence. Consistent icosahedral capsid structures (other than occasional differences in handedness) were obtained by repeating the random model process. Particles with inconsistent/unstable view parameters in the initial refinements were excluded in further image processing. The orientation and center parameters were then transferred to the un-binned images for high-resolution refinements which included Simplex method-based orientation/center optimization and grid search-based refinement of defocus, astigmatism, and magnification of the images. All image refinement and reconstructions were performed with in-house developed programs jspr.py (for overall work-flow), jalign (for 2D alignment) and j3dr (for 3D reconstruction), which use EMAN and EMAN2 library functions.
|3D reconstruction||Algorithm: Projection matching / Software: jspr, EMAN, EMAN2 / CTF correction: Each particle|
Details: For 3D reconstruction, whole datasets were divided into even and odd halves and the initial de novo models and subsequent iterative refinements were all independently performed for each half dataset.
Resolution: 3.6 Å / Resolution method: FSC 0.143, gold-standard
-Atomic model buiding
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-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
+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
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi