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- EMDB-0095: Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the buddi... -

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Basic information

Entry
Database: EMDB / ID: EMD-0095
TitleCryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore
Map dataCBF3-core-Ndc10-DBD
Sample
  • Complex: CBF3-core-Ndc10-DBD complex
    • Protein or peptide: x 5 types
  • Ligand: x 6 types
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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / mitotic spindle elongation ...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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / vacuolar acidification / kinetochore assembly / condensed chromosome, centromeric region / regulation of metabolic process / exit from mitosis / spindle pole body / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / DNA binding, bending / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / mitotic spindle assembly checkpoint signaling / DNA replication origin binding / regulation of mitotic cell cycle / cullin family protein binding / 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 / spindle / kinetochore / G2/M transition of mitotic cell cycle / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / chromosome, telomeric region / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. ...: / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Integrase/recombinase, N-terminal / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Centromere DNA-binding protein complex CBF3 subunit A / Centromere DNA-binding protein complex CBF3 subunit C / Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYan K / Zhang Z / Yang J / McLaughlin SH / Barford D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MRC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2018
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
DepositionJul 1, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseDec 5, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
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  • Surface level: 0.05
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6gyp
  • Surface level: 0.05
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0095.png

Downloads & links

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Map

FileDownload / File: emd_0095.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCBF3-core-Ndc10-DBD
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.41150066 - 0.61012393
Average (Standard dev.)0.00017868022 (±0.0071817855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.4120.6100.000

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Supplemental data

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Sample components

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Entire : CBF3-core-Ndc10-DBD complex

EntireName: CBF3-core-Ndc10-DBD complex
Components
  • Complex: CBF3-core-Ndc10-DBD complex
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit C
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
    • Protein or peptide: Suppressor of kinetochore protein 1
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit A
  • Ligand: METHIONINE
  • Ligand: PHENYLALANINE
  • Ligand: ASPARAGINE
  • Ligand: ARGININE
  • Ligand: THREONINE
  • Ligand: GLUTAMINE

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Supramolecule #1: CBF3-core-Ndc10-DBD complex

SupramoleculeName: CBF3-core-Ndc10-DBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: unidentified baculovirus

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Macromolecule #1: Centromere DNA-binding protein complex CBF3 subunit B

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 71.439891 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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Macromolecule #2: Centromere DNA-binding protein complex CBF3 subunit C

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 56.416863 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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Macromolecule #3: Centromere DNA-binding protein complex CBF3 subunit B

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 66.401859 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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Macromolecule #4: Suppressor of kinetochore protein 1

MacromoleculeName: Suppressor of kinetochore protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 22.35727 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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Macromolecule #5: Centromere DNA-binding protein complex CBF3 subunit A

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 112.066031 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: 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

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Macromolecule #6: METHIONINE

MacromoleculeName: METHIONINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: MET
Molecular weightTheoretical: 149.211 Da
Chemical component information

ChemComp-MET:
METHIONINE / Methionine

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Macromolecule #7: PHENYLALANINE

MacromoleculeName: PHENYLALANINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: PHE
Molecular weightTheoretical: 165.189 Da
Chemical component information

ChemComp-PHE:
PHENYLALANINE / Phenylalanine

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Macromolecule #8: ASPARAGINE

MacromoleculeName: ASPARAGINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ASN
Molecular weightTheoretical: 132.118 Da
Chemical component information

ChemComp-ASN:
ASPARAGINE / Asparagine

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Macromolecule #9: ARGININE

MacromoleculeName: ARGININE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ARG
Molecular weightTheoretical: 175.209 Da
Chemical component information

ChemComp-ARG:
ARGININE / Arginine

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Macromolecule #10: THREONINE

MacromoleculeName: THREONINE / type: ligand / ID: 10 / Number of copies: 2 / Formula: THR
Molecular weightTheoretical: 119.119 Da
Chemical component information

ChemComp-THR:
THREONINE / Threonine

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Macromolecule #11: GLUTAMINE

MacromoleculeName: GLUTAMINE / type: ligand / ID: 11 / Number of copies: 1 / Formula: GLN
Molecular weightTheoretical: 146.144 Da
Chemical component information

ChemComp-GLN:
GLUTAMINE / Glutamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 27.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Initial model was from SIMPLE_PRIME.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73894

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-6gyp:
Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore

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