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- EMDB-20271: Structure of the K. lactis CBF3 core - Ndc10 D1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20271
TitleStructure of the K. lactis CBF3 core - Ndc10 D1 complex
Map dataK. lactis CBF3 core - Ndc10 D1 complex
Sample
  • Complex: K. lactis CBF3 core - Ndc10 D1 complex
    • Protein or peptide: Ndc10
    • Protein or peptide: Ctf13
    • Protein or peptide: Skp1
    • Protein or peptide: Cep3
Keywordsyeast centromere-binding complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA binding / zinc ion binding / nucleus / membrane
Similarity search - Function
: / 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 / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily ...: / 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 / 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 / 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
Similarity search - Domain/homology
E3 ubiquitin ligase complex SCF subunit / KLLA0F13816p / KLLA0E03807p / KLLA0D09977p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLee PD / Wei H
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J Mol Biol / Year: 2019
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
DepositionJun 6, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseSep 18, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p7w
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20271.png

Downloads & links

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Map

FileDownload / File: emd_20271.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationK. lactis CBF3 core - Ndc10 D1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 288 pix.
= 305.424 Å		1.06 Å/pix.
x 288 pix.
= 305.424 Å		1.06 Å/pix.
x 288 pix.
= 305.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0605 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.028194346 - 0.059118193
Average (Standard dev.)0.00013470373 (±0.0014574879)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 305.424 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06051.06051.0605
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z305.424305.424305.424
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0280.0590.000

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Supplemental data

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Half map: K. lactis CBF3 core - Ndc10 D1 complex, half map 1

Fileemd_20271_half_map_1.map
AnnotationK. lactis CBF3 core - Ndc10 D1 complex, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: K. lactis CBF3 core - Ndc10 D1 complex, half map 2

Fileemd_20271_half_map_2.map
AnnotationK. lactis CBF3 core - Ndc10 D1 complex, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : K. lactis CBF3 core - Ndc10 D1 complex

EntireName: K. lactis CBF3 core - Ndc10 D1 complex
Components
  • Complex: K. lactis CBF3 core - Ndc10 D1 complex
    • Protein or peptide: Ndc10
    • Protein or peptide: Ctf13
    • Protein or peptide: Skp1
    • Protein or peptide: Cep3

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Supramolecule #1: K. lactis CBF3 core - Ndc10 D1 complex

SupramoleculeName: K. lactis CBF3 core - Ndc10 D1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Kluyveromyces lactis (yeast)

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Macromolecule #1: Ndc10

MacromoleculeName: Ndc10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 47.053719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKLDSLLKE LPTRTAHLYR SIWHKYTEWL KTMPDLTGAD LKLFLSQKYI VKYIASHDDI AKDPLPTCDA MIWFSRALDI ENNDVLVLQ QRLYGLVKLL EFDYSNVIAI LQKISINLWN PSTDSLQSKH FKTCQDKLKL LLDFQWKFNT NVSFEDRTTV S LKDLQCIL ...String:
MSKLDSLLKE LPTRTAHLYR SIWHKYTEWL KTMPDLTGAD LKLFLSQKYI VKYIASHDDI AKDPLPTCDA MIWFSRALDI ENNDVLVLQ QRLYGLVKLL EFDYSNVIAI LQKISINLWN PSTDSLQSKH FKTCQDKLKL LLDFQWKFNT NVSFEDRTTV S LKDLQCIL DDENGKCGLA HSSKPNFVLV PNFQSPFTCP IFTMAVYYYL RFHGVKKYYK GDGYQILSQL EHIPIIRGKS LD QYPRELT LGNWYPTIFK YCQLPYTKKH WFQVNQEWPQ FPDFSDSSEN TSTLAESDSE NTIGIPDFYI EKMNRTKLQP CPQ VHVHLF PTDLPPDIQA VFDLLNSVLV TSLPLLYRVF PTHDIFLDPS LKTPQNIAFL TGTLPLDIES QEHLLAQLID KTGT VSEIG SG

UniProtKB: KLLA0E03807p

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Macromolecule #2: Ctf13

MacromoleculeName: Ctf13 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 46.159945 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #3: Skp1

MacromoleculeName: Skp1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 21.081141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
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

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Macromolecule #4: Cep3

MacromoleculeName: Cep3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 74.165312 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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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

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63177
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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