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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20270 | |||||||||
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Title | Structure of the K. lactis CBF3 core | |||||||||
![]() | K. lactis CBF3 core | |||||||||
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![]() | yeast centromere-binding complex / ![]() | |||||||||
Function / homology | ![]() 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 / zinc ion binding / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lee PD / Wei H | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.3 KB | Display | ![]() |
Images | ![]() | 63 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 71.2 MB 71.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p7vMC ![]() 6p7wC ![]() 6p7xC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | K. lactis CBF3 core | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: K. lactis CBF3 core, half map 1
File | emd_20270_half_map_1.map | ||||||||||||
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Annotation | K. lactis CBF3 core, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: K. lactis CBF3 core, half map 2
File | emd_20270_half_map_2.map | ||||||||||||
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Annotation | K. lactis CBF3 core, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : K. lactis CBF3 core
Entire | Name: K. lactis CBF3 core |
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Components |
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-Supramolecule #1: K. lactis CBF3 core
Supramolecule | Name: K. lactis CBF3 core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Ctf13
Macromolecule | Name: Ctf13 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.159945 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MFDTKLFLSL PIDIRYTVYF FLGDVVQNVR PPAKSDIFND ELIAYPNIRE FNQSLVDKYS KHIGVYDYIP NFIPNWCRDF DLLRHDIIL TDRLRVCLQY EEQWFSVQWI VVSGELEIGI FTTDEQFLQV SYTINEYCHL LSIAQQDLRL GINVSDINDV N ELCKEIQH ...String: MFDTKLFLSL PIDIRYTVYF FLGDVVQNVR PPAKSDIFND ELIAYPNIRE FNQSLVDKYS KHIGVYDYIP NFIPNWCRDF DLLRHDIIL TDRLRVCLQY EEQWFSVQWI VVSGELEIGI FTTDEQFLQV SYTINEYCHL LSIAQQDLRL GINVSDINDV N ELCKEIQH RWLFDTVSYI SFINCWDLDH ENVVSIIPCM ESFNNLHMLR IESKNMFNNL INTQGVRENP GKTIVYNVRQ NI FELELYT LRDLGYKSVV DLQKWEQLQC LSLSGCEFID LNNLILPQHC KMLILKEVKY IIWWDLSHLL KRIRPQWIIN GQV KKPTKK EEEEESEWYN LYLEVVQTYQ PLNFIELHNA KRVKGNLILP ARLVTESRIK ISNGTKVDSV LLI UniProtKB: KLLA0F13816p |
-Macromolecule #2: Skp1
Macromolecule | Name: Skp1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.081141 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKENQNVVL VSVEGERFVV DRKIAERSLL LKNYLQDLNS GDLHDDNDAD DDEDDEEDGD DEIVMPVPNV RSSVLQKVIE WAVHHKDSN FPDEDDDDSR KAAPVDPWDR EFLKVDQEML YEIILAANYL NIKPLLDAGC KVVAEMIRGR TPEEIRRTFN I VNDFTPEE EAAIRRENEW AEDR UniProtKB: E3 ubiquitin ligase complex SCF subunit |
-Macromolecule #3: Cep3
Macromolecule | Name: Cep3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 74.165312 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKPKISLTK GKHPCTFCQA RKVKCDRSLP ACQNCIERNV TELCEYDDNG SRKRARLADD VNLYDKKLFN IWNQYERLWI HDTLGQCQQ GVYMGIAFPL DVSEYNNTKD FYGYECLFSK ESIFKILDHS LERLGWLYFG FFTDISELPY QMERYWNEYE S MNINLENE ...String: MSKPKISLTK GKHPCTFCQA RKVKCDRSLP ACQNCIERNV TELCEYDDNG SRKRARLADD VNLYDKKLFN IWNQYERLWI HDTLGQCQQ GVYMGIAFPL DVSEYNNTKD FYGYECLFSK ESIFKILDHS LERLGWLYFG FFTDISELPY QMERYWNEYE S MNINLENE EATTRQTTFK KSADQILWDL VLRSVIVMTI YYMPAKSILS LVDIDAIEKY PLDFSESNEG VDELKKKYEI FD YCLRHTL NKVLRTIFTL PPDVRTLQIF LILSNTNFLQ IYPSLGNNIL VHCIHLAKVL GIKDFKLKIN DSGSTRLQKL SMH NIWFRL STVDYMRSSP NKIIALHTDN SSALTRKTLF THCSIDSIDV YDVESNLEVL RWKITSLDRD LEVSEPSLKT LKAM KELLG LLDRKTSVSN DASFNTKFES FFLKLQCNFV MWKILRYEFM QYGVTNGLQK LCCPARRIIA LVANFLKEDY FEYTT HPFC VHILCVIAGF FSFYCIFHEA DEVRDLRNDA VGLLKLLFDP LRPVISCFFS NLSRLEELRH IWKSVEITDQ ANRLVH PVM YVLKTDIIKL KRNLEIISGS LKDANYQETF KDKLEIDINT PALSSDFLEV VREFNLSHPL DINGKMSRQN N UniProtKB: KLLA0D09977p |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 65.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |