+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12993 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cenp-A nucleosome in complex with Cenp-C | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Kinetochore / Nucleosome / Complex / CELL CYCLE | |||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Yan K / Yang J | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Cenp-A nucleosome in complex with Cenp-C Authors: Yan K / Yang J / Zhang Z / Barford D | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12993.map.gz | 9.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12993-v30.xml emd-12993.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
Images | emd_12993.png | 100 KB | ||
Filedesc metadata | emd-12993.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12993 | HTTPS FTP |
-Validation report
Summary document | emd_12993_validation.pdf.gz | 369.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_12993_full_validation.pdf.gz | 368.6 KB | Display | |
Data in XML | emd_12993_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_12993_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12993 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12993 | HTTPS FTP |
-Related structure data
Related structure data | 7on1MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_12993.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Cenp-A nucleosome in complex with Cenp-C
+Supramolecule #1: Cenp-A nucleosome in complex with Cenp-C
+Supramolecule #2: Kinetochore subunit
+Supramolecule #3: Histones
+Supramolecule #4: DNA (152-MER), DNA (123-MER)
+Macromolecule #1: BJ4_G0006610.mRNA.1.CDS.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2B
+Macromolecule #4: BJ4_G0007000.mRNA.1.CDS.1
+Macromolecule #5: Histone H2A
+Macromolecule #6: DNA (152-MER)
+Macromolecule #7: DNA (123-MER)
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124953 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |