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- EMDB-0097: Cryo-EM structure of the CBF3-msk complex of the budding yeast ki... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0097 | |||||||||
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Title | Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore | |||||||||
![]() | CBF3-msk | |||||||||
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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 / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Yan K / Zhang Z / Yang J / McLaughlin SH / Barford D | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
Images | ![]() | 30.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 218.7 KB | Display | ![]() |
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Full document | ![]() | 217.8 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gyuMC ![]() 0095C ![]() 0096C ![]() 6gypC ![]() 6gysC 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 | CBF3-msk | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : CBF3-msk complex
Entire | Name: CBF3-msk complex |
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Components |
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-Supramolecule #1: CBF3-msk complex
Supramolecule | Name: CBF3-msk complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 71.439891 KDa |
Recombinant expression | Organism: ![]() |
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 SDILS |
-Macromolecule #2: Centromere DNA-binding protein complex CBF3 subunit C
Macromolecule | Name: Centromere DNA-binding protein complex CBF3 subunit C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 56.416863 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MPSFNPVRFL ELPIDIRKEV YFHLDGNFCG AHPYPIDILY KSNDVELPGK PSYKRSKRSK KLLRYMYPVF ATYLNIFEYS PQLIEKWLE YAFWLRYDCL VLDCFKVNHL YDGTLIDALE WTYLDNELRL AYFNKASMLE VWYTFKEYKK WVIDSVAFDE L DLLNVSNI ...String: MPSFNPVRFL ELPIDIRKEV YFHLDGNFCG AHPYPIDILY KSNDVELPGK PSYKRSKRSK KLLRYMYPVF ATYLNIFEYS PQLIEKWLE YAFWLRYDCL VLDCFKVNHL YDGTLIDALE WTYLDNELRL AYFNKASMLE VWYTFKEYKK WVIDSVAFDE L DLLNVSNI QFNIDNLTPQ LVDKCLSILE QKDLFATIGE VQFGQDEEVG EEKDVDVSGA NSDENSSPSS TIKNKKRSAS KR SHSDNGN VGATHNQLTS ISVIRTIRSM ESMKSLRKIT VRGEKLYELL INFHGFRDNP GKTISYIVKR RINEIRLSRM NQI SRTGLA DFTRWDNLQK LVLSRVAYID LNSIVFPKNF KSLTMKRVSK IKWWNIEENI LKELKVDKRT FKSLYIKEDD SKFT KFFNL RHTRIKELDK SEINQITYLR CQAIVWLSFR TLNHIKLQNV SEVFNNIIVP RALFDSKRVE IYRCEKISQV LVI |
-Macromolecule #3: Centromere DNA-binding protein complex CBF3 subunit B
Macromolecule | Name: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 66.401859 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFNRITASSS KEYLPDLLLF WQNYEYWITN IGLYKTKQRD LTRTPANLDT DTEECMFWMN YLQKDQSFQL MNFAMENLGA LYFGSIGDI SELYLRVEQY WDRRADKNHS VDGKYWDALI WSVFTMCIYY MPVEKLAEIF SVYPLHEYLG SNKRLNWEDG M QLVMCQNF ...String: MFNRITASSS KEYLPDLLLF WQNYEYWITN IGLYKTKQRD LTRTPANLDT DTEECMFWMN YLQKDQSFQL MNFAMENLGA LYFGSIGDI SELYLRVEQY WDRRADKNHS VDGKYWDALI WSVFTMCIYY MPVEKLAEIF SVYPLHEYLG SNKRLNWEDG M QLVMCQNF ARCSLFQLKQ CDFMAHPDIR LVQAYLILAT TTFPYDEPLL ANSLLTQCIH TFKNFHVDDF RPLLNDDPVE SI AKVTLGR IFYRLCGCDY LQSGPRKPIA LHTEVSSLLQ HAAYLQDLPN VDVYREENST EVLYWKIISL DRDLDQYLNK SSK PPLKTL DAIRRELDIF QYKVDSLEED FRSNNSRFQK FIALFQISTV SWKLFKMYLI YYDTADSLLK VIHYSKVIIS LIVN NFHAK SEFFNRHPMV MQTITRVVSF ISFYQIFVES AAVKQLLVDL TELTANLPTI FGSKLDKLVY LTERLSKLKL LWDKV QLLD SGDSFYHPVF KILQNDIKII ELKNDEMFSL IKGLGSLVPL NKLRQESLLE EEDENNTEPS DFRTIVEEFQ SEYNIS DIL S |
-Macromolecule #4: Suppressor of kinetochore protein 1
Macromolecule | Name: Suppressor of kinetochore protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 22.35727 KDa |
Recombinant expression | Organism: ![]() |
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 #5: Centromere DNA-binding protein complex CBF3 subunit A
Macromolecule | Name: Centromere DNA-binding protein complex CBF3 subunit A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 112.066031 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRSSILFLLK LMKIMDVQQQ QEAMSSEDRF QELVDSLKPR TAHQYKTYYT KYIQWCQLNQ IIPTPEDNSV NSVPYKDLPI SAELIHWFL LDTLITDDKP GEKREETEDL DEEEENSFKI ATLKKIIGSL NFLSKLCKVH ENPNANIDTK YLESVTKLHT H WIDSQKAI ...String: MRSSILFLLK LMKIMDVQQQ QEAMSSEDRF QELVDSLKPR TAHQYKTYYT KYIQWCQLNQ IIPTPEDNSV NSVPYKDLPI SAELIHWFL LDTLITDDKP GEKREETEDL DEEEENSFKI ATLKKIIGSL NFLSKLCKVH ENPNANIDTK YLESVTKLHT H WIDSQKAI TTNETNNTNT QVLCPPLLKV SLNLWNPETN HLSEKFFKTC SEKLRFLVDF QLRSYLNLSF EERSKIRFGS LK LGKRDRD AIIYHKVTHS AEKKDTPGHH QLLALLPQDC PFICPQTTLA AYLYLRFYGI PSVSKGDGFP NLNADENGSL LQD IPILRG KSLTTYPREE TFSNYYTTVF RYCHLPYKRR EYFNKCNLVY PTWDEDTFRT FFNEENHGNW LEQPEAFAFP DKIP FDFKK IMNFKSPYTS YSTNAKKDPF PPPKDLLVQI FPEIDEYKRH DYEGLSQNSR DFLDLMEVLR ERFLSNLPWI YKFFP NHDI FQDPIFGNSD FQSYFNDKTI HSKGSPILSF DILPGFNKIY KNKTNFYSLL IERPSQLTFA SSHNPDTHPT QKQESE GPL QMSQLDTTQL NELLKQQSFE YVQFQTLSNF QILLSVFNKI FEKLEMKKSS RGYILHQLNL FKITLDERIK KSKIDDA DK FIRDNQPIKK EENIVNEDGP NTSRRTKRPK QIRLLSIADS SDESSTEDSN VFKKDGESIE DGAYGENEDE NDSEMQEQ L KSMINELINS KISTFLRDQM DQFELKINAL LDKILEEKVT RIIEQKLGSH TGKFSTLKRP QLYMTEEHNV GFDMEVPKK LRTSGKYAET VKDNDDHQAM STTASPSPEQ DQEAKSYTDE QEFMLDKSID SIEGIILEWF TPNAKYANQC VHSMNKSGNK SWRANCEAL YKERKSIVEF YIYLVNHESL DRYKAVDICE KLRDQNEGSF SRLAKFLRKW RHDHQNSFDG LLVYLSN |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER Details: Initial model was from SIMPLE_PRIME reconstruction. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198010 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |