|Entry||Database: PDB / ID: 6o2k|
|Title||Drosophila melanogaster CENP-C cupin domain|
|Components||Centromeric protein-C, isoform A|
|Keywords||CELL CYCLE / Cupin / Kinetochore / CENP-C / Drosophila / dimer|
|Function / homology|
Function and homology information
regulation of stem cell differentiation / regulation of centromere complex assembly / kinetochore assembly / condensed chromosome, centromeric region / protein localization to chromosome, centromeric region / female meiosis chromosome segregation / protein localization to kinetochore / mitotic metaphase plate congression / chromosome, centromeric region / kinetochore / chromosome segregation
Similarity search - Function
Centromeric protein-C, isoform A
Similarity search - Component
|Biological species||Drosophila melanogaster (fruit fly)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å|
|Authors||Chik, J.K. / Cho, U.S.|
|Funding support|| United States, 2items |
|Citation||Journal: J.Biol.Chem. / Year: 2019|
Title: Structures of CENP-C cupin domains at regional centromeres reveal unique patterns of dimerization and recruitment functions for the inner pocket.
Authors: Chik, J.K. / Moiseeva, V. / Goel, P.K. / Meinen, B.A. / Koldewey, P. / An, S. / Mellone, B.G. / Subramanian, L. / Cho, U.S.
|Structure viewer||Molecule: |
Downloads & links
A: Centromeric protein-C, isoform A
B: Centromeric protein-C, isoform A
Mass: 16073.384 Da / Num. of mol.: 2 / Fragment: Cupin Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Cenp-C, CENP-C, cenp-C, Cenp-C-RA, CenpC, CG11745, CG11746, CLD1, Dmel\CG31258, l(2)SH3 157, l(3)85Aa, l(3)SH157, L1, CG31258, Dmel_CG31258
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VHP9
|#2: Water|| ChemComp-HOH / ||Sequence details||The construct used for crystallization was D. melanogaster CENP-C 1190-1411 with an additional Ser- ...The construct used for crystallization was D. melanogaster CENP-C 1190-1411 with an additional Ser-Asn-Ala sequence at the N-terminus from the expression tag. Tag and residues 1190-1269 were likely proteolytically cleaved during crystallization and are not visible in the structure.|
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 2|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→30.86 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.7 |
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 1.81→30.86 Å|
|Refine LS restraints|
|LS refinement shell|
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- 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.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+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
+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.
- 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
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.
- 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