[English] 日本語
- PDB-1k3k: Solution Structure of a Bcl-2 Homolog from Kaposi's Sarcoma Virus -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 1k3k
TitleSolution Structure of a Bcl-2 Homolog from Kaposi's Sarcoma Virus
Componentsfunctional anti-apoptotic factor vBCL-2 homolog
KeywordsAPOPTOSIS / Bcl-2 / herpesvirus / solution structure
Function / homologyBcl2-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 sourceHuman herpesvirus 8
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, Q. / Petros, A.M. / Virgin, H.W. / Fesik, S.W. / Olejniczak, E.T.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2001 / Release: Apr 10, 2002
RevisionDateData content typeGroupProviderType
1.0Apr 10, 2002Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: functional anti-apoptotic factor vBCL-2 homolog

Theoretical massNumber of molelcules
Total (without water)17,7581
NMR ensembles
Number of conformers (submitted / calculated)1 / 100AVERAGE, MINIMIZED


#1: Protein/peptide functional anti-apoptotic factor vBCL-2 homolog

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

Experimental details


ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions IDExperiment IDSolution IDType

Sample preparation

DetailsContents: 0.5-1.0 MM PROTEIN, 20 mM2 H-TRIS, 5 mM2 H-dithiothreitol
sample conditionsIonic strength: 20 mM / pH: 7.8 / Pressure: ATMOSPHERIC atm / Temperature: 298 K
Crystal grow
Method: other / Details: NMR

NMR measurement

RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strengthSpectrometer ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003


NMR software
CNXstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE, MINIMIZED / Conformers calculated total number: 100 / Conformers submitted total number: 1

About Yorodumi


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

External links: EMDB at PDBe / Contact to PDBj

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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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

Read more


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

Read more