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Yorodumi- EMDB-0095: Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the buddi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0095 | |||||||||
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Title | Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore | |||||||||
Map data | CBF3-core-Ndc10-DBD | |||||||||
Sample |
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Function / homology | Function and homology information RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / mitotic spindle elongation / centromeric DNA binding ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / regulation of exit from mitosis / kinetochore assembly / condensed chromosome, centromeric region / positive regulation of glucose transmembrane transport / regulation of metabolic process / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / vacuolar acidification / silent mating-type cassette heterochromatin formation / DNA binding, bending / spindle pole body / mitochondrial fusion / exit from mitosis / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / mitotic spindle assembly checkpoint signaling / Orc1 removal from chromatin / regulation of mitotic cell cycle / cullin family protein binding / DNA replication origin binding / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / spindle midzone / endomembrane system / negative regulation of cytoplasmic translation / chromosome segregation / G1/S transition of mitotic cell cycle / kinetochore / G2/M transition of mitotic cell cycle / spindle / mitotic cell cycle / chromosome, telomeric region / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Yan K / Zhang Z / Yang J / McLaughlin SH / Barford D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Architecture of the CBF3-centromere complex of the budding yeast kinetochore. Authors: Kaige Yan / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford / Abstract: Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into ...Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0095.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-0095-v30.xml emd-0095.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_0095.png | 30.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0095 | HTTPS FTP |
-Validation report
Summary document | emd_0095_validation.pdf.gz | 209 KB | Display | EMDB validaton report |
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Full document | emd_0095_full_validation.pdf.gz | 208.1 KB | Display | |
Data in XML | emd_0095_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0095 | HTTPS FTP |
-Related structure data
Related structure data | 6gypMC 0096C 0097C 6gysC 6gyuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0095.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CBF3-core-Ndc10-DBD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : CBF3-core-Ndc10-DBD complex
+Supramolecule #1: CBF3-core-Ndc10-DBD complex
+Macromolecule #1: Centromere DNA-binding protein complex CBF3 subunit B
+Macromolecule #2: Centromere DNA-binding protein complex CBF3 subunit C
+Macromolecule #3: Centromere DNA-binding protein complex CBF3 subunit B
+Macromolecule #4: Suppressor of kinetochore protein 1
+Macromolecule #5: Centromere DNA-binding protein complex CBF3 subunit A
+Macromolecule #6: METHIONINE
+Macromolecule #7: PHENYLALANINE
+Macromolecule #8: ASPARAGINE
+Macromolecule #9: ARGININE
+Macromolecule #10: THREONINE
+Macromolecule #11: GLUTAMINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 27.0 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: OTHER / Details: Initial model was from SIMPLE_PRIME. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73894 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-6gyp: |