+Open data
-Basic information
Entry | Database: PDB / ID: 6p7x | |||||||||
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Title | Structure of the K. lactis CBF3 core - Ndc10 D1D2 complex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / yeast centromere-binding complex | |||||||||
Function / homology | Function and homology information SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / mitotic cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / DNA binding / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Kluyveromyces lactis (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Lee, P.D. / Wei, H. / Tan, D. / Harrison, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Mol Biol / Year: 2019 Title: Structure of the Centromere Binding Factor 3 Complex from Kluyveromyces lactis. Authors: Phong D Lee / Hui Wei / Dongyan Tan / Stephen C Harrison / Abstract: Kinetochores are the multiprotein complexes that link chromosomal centromeres to mitotic-spindle microtubules. Budding yeast centromeres comprise three sequential "centromere-determining elements", ...Kinetochores are the multiprotein complexes that link chromosomal centromeres to mitotic-spindle microtubules. Budding yeast centromeres comprise three sequential "centromere-determining elements", CDEI, II, and III. CDEI (8 bp) and CDEIII (∼25 bp) are conserved between Kluyveromyces lactis and Saccharomyces cerevisiae, but CDEII in the former is twice as long (160 bp) as CDEII in the latter (80 bp). The CBF3 complex recognizes CDEIII and is required for assembly of a centromeric nucleosome, which in turn recruits other kinetochore components. To understand differences in centromeric nucleosome assembly between K. lactis and S. cerevisiae, we determined the structure of a K. lactis CBF3 complex by electron cryomicroscopy at ∼4 Å resolution and compared it with published structures of S. cerevisiae CBF3. We show differences in the pose of Ndc10 and discuss potential models of the K. lactis centromeric nucleosome that account for the extended CDEII length. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6p7x.cif.gz | 709.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p7x.ent.gz | 590.3 KB | Display | PDB format |
PDBx/mmJSON format | 6p7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p7x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6p7x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6p7x_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 6p7x_validation.cif.gz | 95.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7x ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7x | HTTPS FTP |
-Related structure data
Related structure data | 20272MC 6p7vC 6p7wC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 47053.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_E03807g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPM4 |
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#2: Protein | Mass: 46159.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_F13816g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CK37 |
#3: Protein | Mass: 21081.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: SKP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94228 |
#4: Protein | Mass: 74165.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_D09977g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CRD4 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: K. lactis CBF3 core - Ndc10 D1D2 Complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Kluyveromyces lactis (yeast) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63177 / Symmetry type: POINT |