+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4163 | ||||||||||||
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Title | CBF3 Core Complex | ||||||||||||
Map data | CBF3 core | ||||||||||||
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 / centromeric DNA binding / regulation of exit from mitosis ...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 / centromeric DNA binding / regulation of exit from mitosis / kinetochore assembly / 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 / 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 / endomembrane system / negative regulation of cytoplasmic translation / G1/S transition of mitotic cell cycle / kinetochore / G2/M transition of mitotic cell cycle / 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 / zinc ion binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Leber V / Singleton MR | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: EMBO J / Year: 2018 Title: Structural basis for assembly of the CBF3 kinetochore complex. Authors: Vera Leber / Andrea Nans / Martin R Singleton / Abstract: Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the ...Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the presence of nucleosomes containing the histone H3 variant, CENP-A. In budding yeast, centromere establishment begins with the recognition of a specific DNA sequence by the CBF3 complex. This in turn facilitates CENP-A nucleosome deposition and kinetochore assembly. Here, we describe a 3.6 Å single-particle cryo-EM reconstruction of the core CBF3 complex, incorporating the sequence-specific DNA-binding protein Cep3 together with regulatory subunits Ctf13 and Skp1. This provides the first structural data on Ctf13, defining it as an F-box protein of the leucine-rich-repeat family, and demonstrates how a novel F-box-mediated interaction between Ctf13 and Skp1 is responsible for initial assembly of the CBF3 complex. | ||||||||||||
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_4163.map.gz | 49.3 MB | EMDB map data format | |
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Header (meta data) | emd-4163-v30.xml emd-4163.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4163_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_4163.png | 42.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4163 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4163 | HTTPS FTP |
-Validation report
Summary document | emd_4163_validation.pdf.gz | 322.4 KB | Display | EMDB validaton report |
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Full document | emd_4163_full_validation.pdf.gz | 321.5 KB | Display | |
Data in XML | emd_4163_validation.xml.gz | 10.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4163 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4163 | HTTPS FTP |
-Related structure data
Related structure data | 6f07MC 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_4163.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CBF3 core | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.078 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 Complex
Entire | Name: CBF3 Core Complex |
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Components |
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-Supramolecule #1: CBF3 Core Complex
Supramolecule | Name: CBF3 Core Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: Centromere DNA-binding protein complex CBF3 subunit B
Macromolecule | Name: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 72.637117 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MFNRTTQLKS KHPCSVCTRR KVKCDRMIPC GNCRKRGQDS ECMKSTKLIT ASSSKEYLPD LLLFWQNYEY WITNIGLYKT KQRDLTRTP ANLDTDTEEC MFWMNYLQKD QSFQLMNFAM ENLGALYFGS IGDISELYLR VEQYWDRRAD KNHSVDGKYW D ALIWSVFT ...String: MFNRTTQLKS KHPCSVCTRR KVKCDRMIPC GNCRKRGQDS ECMKSTKLIT ASSSKEYLPD LLLFWQNYEY WITNIGLYKT KQRDLTRTP ANLDTDTEEC MFWMNYLQKD QSFQLMNFAM ENLGALYFGS IGDISELYLR VEQYWDRRAD KNHSVDGKYW D ALIWSVFT MCIYYMPVEK LAEIFSVYPL HEYLGSNKRL NWEDGMQLVM CQNFARCSLF QLKQCDFMAH PDIRLVQAYL IL ATTTFPY DEPLLANSLL TQCIHTFKNF HVDDFRPLLN DDPVESIAKV TLGRIFYRLC GCDYLQSGPR KPIALHTEVS SLL QHAAYL QDLPNVDVYR EENSTEVLYW KIISLDRDLD QYLNKSSKPP LKTLDAIRRE LDIFQYKVDS LEEDFRSNNS RFQK FIALF QISTVSWKLF KMYLIYYDTA DSLLKVIHYS KVIISLIVNN FHAKSEFFNR HPMVMQTITR VVSFISFYQI FVESA AVKQ LLVDLTELTA NLPTIFGSKL DKLVYLTERL SKLKLLWDKV QLLDSGDSFY HPVFKILQND IKIIELKNDE MFSLIK GLG SLVPLNKLRQ ESLLEEEDEN NTEPSDFRTI VEEFQSEYNI SDILSGSGGS GENLYFQ |
-Macromolecule #2: Suppressor of kinetochore protein 1
Macromolecule | Name: Suppressor of kinetochore protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 22.35727 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MVTSNVVLVS GEGERFTVDK KIAERSLLLK NYLNDMHDSN LQNNSDSESD SDSETNHKSK DNNNGDDDDE DDDEIVMPVP NVRSSVLQK VIEWAEHHRD SNFPDEDDDD SRKSAPVDSW DREFLKVDQE MLYEIILAAN YLNIKPLLDA GCKVVAEMIR G RSPEEIRR ...String: MVTSNVVLVS GEGERFTVDK KIAERSLLLK NYLNDMHDSN LQNNSDSESD SDSETNHKSK DNNNGDDDDE DDDEIVMPVP NVRSSVLQK VIEWAEHHRD SNFPDEDDDD SRKSAPVDSW DREFLKVDQE MLYEIILAAN YLNIKPLLDA GCKVVAEMIR G RSPEEIRR TFNIVNDFTP EEEAAIRREN EWAEDR |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.16 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
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-6f07: |