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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0051 | |||||||||
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Title | Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 | |||||||||
![]() | Reconstruction of the CBF3CCdeltaN (Core complex of CBF3 comprising the homodimer of Cep3deltaN and the heterodimer of Skp1-Ctf13) in complex with domains 1-2 of Ndc10 | |||||||||
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Function / homology | ![]() 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 / regulation of metabolic process / spindle pole body / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / vacuolar acidification / silent mating-type cassette heterochromatin formation / mitochondrial fusion / exit from mitosis / DNA binding, bending / 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 / DNA replication origin binding / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / spindle midzone / endomembrane system / negative regulation of cytoplasmic translation / regulation of mitotic cell cycle / chromosome segregation / kinetochore / spindle / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Zhang WJ / Lukoynova N / Vaughan CK | |||||||||
![]() | ![]() Title: Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. Authors: Wenjuan Zhang / Natalya Lukoyanova / Shomon Miah / Jonathan Lucas / Cara K Vaughan / ![]() Abstract: The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the ...The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the kinetochore in these organisms, as it facilitates genetic centromere specification and allows association of all other kinetochore components. We determined high-resolution structures of the core complex of CBF3 alone and in association with a monomeric construct of Ndc10, using cryoelectron microscopy (cryo-EM). We identify the DNA-binding site of the complex and present a model in which CBF3 induces a tight bend in centromeric DNA, thus facilitating assembly of the centromeric nucleosome. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 129.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 274.4 KB | Display | ![]() |
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Full document | ![]() | 273.5 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gsaMC ![]() 0052C ![]() 4241C ![]() 6fe8C 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
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Annotation | Reconstruction of the CBF3CCdeltaN (Core complex of CBF3 comprising the homodimer of Cep3deltaN and the heterodimer of Skp1-Ctf13) in complex with domains 1-2 of Ndc10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Core CBF3 in complex with Ndc10 D1-2
Entire | Name: Core CBF3 in complex with Ndc10 D1-2 |
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Components |
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-Supramolecule #1: Core CBF3 in complex with Ndc10 D1-2
Supramolecule | Name: Core CBF3 in complex with Ndc10 D1-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length ...Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length heterodimer of Skp1 and Ctf13, and a monomeric construct Ndc10 comprising domains 1-2. |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 286 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 Details: N-terminal polyhistidine purification tagTruncation of the binuclear zinc cluster domain Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 68.454125 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGGSSHHHHH HSSGLVPRGS HMKLITASSS KEYLPDLLLF WQNYEYWITN IGLYKTKQRD LTRTPANLDT DTEECMFWMN YLQKDQSFQ LMNFAMENLG ALYFGSIGDI SELYLRVEQY WDRRADKNHS VDGKYWDALI WSVFTMCIYY MPVEKLAEIF S VYPLHEYL ...String: MGGSSHHHHH HSSGLVPRGS HMKLITASSS KEYLPDLLLF WQNYEYWITN IGLYKTKQRD LTRTPANLDT DTEECMFWMN YLQKDQSFQ LMNFAMENLG ALYFGSIGDI SELYLRVEQY WDRRADKNHS VDGKYWDALI WSVFTMCIYY MPVEKLAEIF S VYPLHEYL GSNKRLNWED GMQLVMCQNF ARCSLFQLKQ CDFMAHPDIR LVQAYLILAT TTFPYDEPLL ANSLLTQCIH TF KNFHVDD FRPLLNDDPV ESIAKVTLGR IFYRLCGCDY LQSGPRKPIA LHTEVSSLLQ HAAYLQDLPN VDVYREENST EVL YWKIIS LDRDLDQYLN KSSKPPLKTL DAIRRELDIF QYKVDSLEED FRSNNSRFQK FIALFQISTV SWKLFKMYLI YYDT ADSLL KVIHYSKVII SLIVNNFHAK SEFFNRHPMV MQTITRVVSF ISFYQIFVES AAVKQLLVDL TELTANLPTI FGSKL DKLV YLTERLSKLK LLWDKVQLLD SGDSFYHPVF KILQNDIKII ELKNDEMFSL IKGLGSLVPL NKLRQESLLE EEDENN TEP SDFRTIVEEF QSEYNISDIL S |
-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: ![]() ![]() |
Molecular weight | Theoretical: 22.558451 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGVTSNVVLV SGEGERFTVD KKIAERSLLL KNYLNDMHDS NLQNNSDSES DSDSETNHKS KDNNNGDDDD EDDDEIVMPV PNVRSSVLQ KVIEWAEHHR DSNFPDEDDD DSRKSAPVDS WDREFLKVDQ EMLYEIILAA NYLNIKPLLD AGCKVVAEMI R GRSPEEIR ...String: MGVTSNVVLV SGEGERFTVD KKIAERSLLL KNYLNDMHDS NLQNNSDSES DSDSETNHKS KDNNNGDDDD EDDDEIVMPV PNVRSSVLQ KVIEWAEHHR DSNFPDEDDD DSRKSAPVDS WDREFLKVDQ EMLYEIILAA NYLNIKPLLD AGCKVVAEMI R GRSPEEIR RTFNIVNDFT PEEEAAIRRE NEWAEDRGS |
-Macromolecule #3: Centromere DNA-binding protein complex CBF3 subunit C
Macromolecule | Name: Centromere DNA-binding protein complex CBF3 subunit C / type: protein_or_peptide / ID: 3 / Details: C-terminal CBP purification tag / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 60.899961 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGPSFNPVRF LELPIDIRKE VYFHLDGNFC GAHPYPIDIL YKSNDVELPG KPSYKRSKRS KKLLRYMYPV FATYLNIFEY SPQLIEKWL EYAFWLRYDC LVLDCFKVNH LYDGTLIDAL EWTYLDNELR LAYFNKASML EVWYTFKEYK KWVIDSVAFD E LDLLNVSN ...String: MGPSFNPVRF LELPIDIRKE VYFHLDGNFC GAHPYPIDIL YKSNDVELPG KPSYKRSKRS KKLLRYMYPV FATYLNIFEY SPQLIEKWL EYAFWLRYDC LVLDCFKVNH LYDGTLIDAL EWTYLDNELR LAYFNKASML EVWYTFKEYK KWVIDSVAFD E LDLLNVSN IQFNIDNLTP QLVDKCLSIL EQKDLFATIG EVQFGQDEEV GEEKDVDVSG ANSDENSSPS STIKNKKRSA SK RSHSDNG NVGATHNQLT SISVIRTIRS MESMKSLRKI TVRGEKLYEL LINFHGFRDN PGKTISYIVK RRINEIRLSR MNQ ISRTGL ADFTRWDNLQ KLVLSRVAYI DLNSIVFPKN FKSLTMKRVS KIKWWNIEEN ILKELKVDKR TFKSLYIKED DSKF TKFFN LRHTRIKELD KSEINQITYL RCQAIVWLSF RTLNHIKLQN VSEVFNNIIV PRALFDSKRV EIYRCEKISQ VLVIG SRSG SENLYFQGSK RRWKKNFIAV SAANRFKKIS SSGAL |
-Macromolecule #4: Centromere DNA-binding protein complex CBF3 subunit A
Macromolecule | Name: Centromere DNA-binding protein complex CBF3 subunit A / type: protein_or_peptide / ID: 4 Details: Domains 1-2 of Ndc10 with a non-cleavable C-terminal StrepII tag Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 66.159578 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGRSSILFLL KLMKIMDVQQ QQEAMSSEDR FQELVDSLKP RTAHQYKTYY TKYIQWCQLN QIIPTPEDNS VNSVPYKDLP ISAELIHWF LLDTLITDDK PGEKREETED LDEEEENSFK IATLKKIIGS LNFLSKLCKV HENPNANIDT KYLESVTKLH T HWIDSQKA ...String: MGRSSILFLL KLMKIMDVQQ QQEAMSSEDR FQELVDSLKP RTAHQYKTYY TKYIQWCQLN QIIPTPEDNS VNSVPYKDLP ISAELIHWF LLDTLITDDK PGEKREETED LDEEEENSFK IATLKKIIGS LNFLSKLCKV HENPNANIDT KYLESVTKLH T HWIDSQKA ITTNETNNTN TQVLCPPLLK VSLNLWNPET NHLSEKFFKT CSEKLRFLVD FQLRSYLNLS FEERSKIRFG SL KLGKRDR DAIIYHKVTH SAEKKDTPGH HQLLALLPQD CPFICPQTTL AAYLYLRFYG IPSVSKGDGF PNLNADENGS LLQ DIPILR GKSLTTYPRE ETFSNYYTTV FRYCHLPYKR REYFNKCNLV YPTWDEDTFR TFFNEENHGN WLEQPEAFAF PDKI PFDFK KIMNFKSPYT SYSTNAKKDP FPPPKDLLVQ IFPEIDEYKR HDYEGLSQNS RDFLDLMEVL RERFLSNLPW IYKFF PNHD IFQDPIFGNS DFQSYFNDKT IHSKGSPILS FDILPGFNKI YKNKTNFYSL LIERPSQLTF ASSHNPDTHP WSHPQF EK |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.15 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I | ||||||||||||
Details | The sample is homogeneous and well-dispersed on grids. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2003 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | "Fit in map" function used to place 6FE8 and 4ACO with out further refinement or model building |
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Output model | ![]() PDB-6gsa: |