|Entry||Database: PDB / ID: 1k3k|
|Title||Solution Structure of a Bcl-2 Homolog from Kaposi's Sarcoma Virus|
|Components||functional anti-apoptotic factor vBCL-2 homolog|
|Keywords||APOPTOSIS / Bcl-2 / herpesvirus / solution structure|
|Function / homology||Bcl2-like / Blc2 family / Blc2-like superfamily / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / negative regulation by symbiont of host apoptotic process / regulation of apoptotic process / integral component of membrane / ORF 16 / Bcl-2|
Function and homology information
|Specimen source||Human herpesvirus 8|
|Method||SOLUTION NMR / simulated annealing|
|Authors||Huang, Q. / Petros, A.M. / Virgin, H.W. / Fesik, S.W. / Olejniczak, E.T.|
|Citation||Journal: Proc.Natl.Acad.Sci.USA / Year: 2002|
Title: Solution structure of a Bcl-2 homolog from Kaposi sarcoma virus.
Authors: Huang, Q. / Petros, A.M. / Virgin, H.W. / Fesik, S.W. / Olejniczak, E.T.
SummaryFull reportAbout validation report
|Date||Deposition: Oct 3, 2001 / Release: Apr 10, 2002|
|Structure viewer||Molecule: |
Downloads & links
A: functional anti-apoptotic factor vBCL-2 homolog
|#1: Protein/peptide|| |
Mass: 17758.215 Da / Num. of mol.: 1 / Mutation: N76D, V117A / Source: (gene. exp.) Human herpesvirus 8 / Genus: Rhadinovirus / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P90504, UniProt: Q76RI8*PLUS
|Experiment||Method: SOLUTION NMR|
|Details||Contents: 0.5-1.0 MM PROTEIN, 20 mM2 H-TRIS, 5 mM2 H-dithiothreitol|
|sample conditions||Ionic strength: 20 mM / pH: 7.8 / Pressure: ATMOSPHERIC atm / Temperature: 298 K|
*PLUSMethod: other / Details: NMR
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M|
|Radiation wavelength||Relative weight: 1|
|Refinement||Method: simulated annealing / Software ordinal: 1|
|NMR ensemble||Conformer selection criteria: AVERAGE, MINIMIZED / Conformers calculated total number: 100 / Conformers submitted total number: 1|
-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