The biological unit is a dimer. There are 5 monomers in the asymmetric unit (chain A, B, C, D and E), which form 5 biological units on application of a 2-fold along 'b' axis.
-
Components
#1: Protein
Capsidprotein
Mass: 14987.403 Da / Num. of mol.: 5 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rubella virus / Strain: M33 / Gene: Capsid / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8QL55, UniProt: P08563*PLUS
Sequence details
N-TERMINAL 20 AMINO ACIDS ASN PRO PHE GLN ALA ALA VAL ALA ARG GLY LEU ARG PRO PRO LEU HIS ASP PRO ...N-TERMINAL 20 AMINO ACIDS ASN PRO PHE GLN ALA ALA VAL ALA ARG GLY LEU ARG PRO PRO LEU HIS ASP PRO ASP THR WERE INCLUDED IN CRYSTALLIZATION SET UP BUT WERE DEGRADED DURING CRYSTALLIZATION
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.53 Å3/Da / Density % sol: 19.7 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 4000, 20% 2-propanol, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
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.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
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