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- EMDB-20200: Cryo-EM structure of the yeast Ctf3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20200
TitleCryo-EM structure of the yeast Ctf3 complex
Map dataFinal volume
Sample
  • Complex: Ctf3 complex
    • Protein or peptide: Inner kinetochore subunit CTF3
    • Protein or peptide: Inner kinetochore subunit MCM16
    • Protein or peptide: Inner kinetochore subunit MCM22
Keywordskinetochore / chromosome / cryo-em / CELL CYCLE
Function / homology
Function and homology information


attachment of spindle microtubules to kinetochore / establishment of mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division / nucleus
Similarity search - Function
Inner kinetochore subunit MCM22 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit CTF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsHinshaw SM / Harrison SC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2019
Title: The structure of the yeast Ctf3 complex.
Authors: Stephen M Hinshaw / Andrew N Dates / Stephen C Harrison /
Abstract: Kinetochores are the chromosomal attachment points for spindle microtubules. They are also signaling hubs that control major cell cycle transitions and coordinate chromosome folding. Most well- ...Kinetochores are the chromosomal attachment points for spindle microtubules. They are also signaling hubs that control major cell cycle transitions and coordinate chromosome folding. Most well-studied eukaryotes rely on a conserved set of factors, which are divided among two loosely-defined groups, for these functions. Outer kinetochore proteins contact microtubules or regulate this contact directly. Inner kinetochore proteins designate the kinetochore assembly site by recognizing a specialized nucleosome containing the H3 variant Cse4/CENP-A. We previously determined the structure, resolved by cryo-electron microscopy (cryo-EM), of the yeast Ctf19 complex (Ctf19c, homologous to the vertebrate CCAN), providing a high-resolution view of inner kinetochore architecture (Hinshaw and Harrison, 2019). We now extend these observations by reporting a near-atomic model of the Ctf3 complex, the outermost Ctf19c sub-assembly seen in our original cryo-EM density. The model is sufficiently well-determined by the new data to enable molecular interpretation of Ctf3 recruitment and function.
History
DepositionMay 4, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 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: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oua
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20200.png

Downloads & links

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Map

FileDownload / File: emd_20200.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal volume
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07739245 - 0.10065111
Average (Standard dev.)-0.000013614005 (±0.0031089573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z217.600217.600217.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0770.101-0.000

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Supplemental data

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Mask #1

Fileemd_20200_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ctf3 complex

EntireName: Ctf3 complex
Components
  • Complex: Ctf3 complex
    • Protein or peptide: Inner kinetochore subunit CTF3
    • Protein or peptide: Inner kinetochore subunit MCM16
    • Protein or peptide: Inner kinetochore subunit MCM22

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Supramolecule #1: Ctf3 complex

SupramoleculeName: Ctf3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Inner kinetochore subunit CTF3

MacromoleculeName: Inner kinetochore subunit CTF3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 84.617891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMSLILDD IILSLTNANE RTPPQALKTT LSLLYEKSKQ YGLSSPQLQA LVRLLCETSI IDTVTKVYIV ENCFLPDGYL TKELLLEII NHLGTPTVFS RYRIQTPPVL QSALCKWLVH VYFLFPVHSE REHNISSSIW LHLWQFSFLQ KWITPLVIWQ A TTPVDVKP ...String:
SNAMSLILDD IILSLTNANE RTPPQALKTT LSLLYEKSKQ YGLSSPQLQA LVRLLCETSI IDTVTKVYIV ENCFLPDGYL TKELLLEII NHLGTPTVFS RYRIQTPPVL QSALCKWLVH VYFLFPVHSE REHNISSSIW LHLWQFSFLQ KWITPLVIWQ A TTPVDVKP WKLSIIKRCA MHPGYRDAPG SATLILQRFQ CLVGASSQIT ESIITINCNR KTLKSHRNLK LDAHFLSILK RI LSRAHPA NFPADTVQNT IDMYLSEIHQ LGADSIYPLR LQSLPEYVPS DSTVSLWDVT SLEQLAQNWP QLHIPNDVDY MMK PSLNSN VLLPRKVMSR DSLKHLYSSI ILIKNSRDES SSPYEWCIWQ LKRCFAHQIE TPQEVIPIII SVSSMDNKLS SRII QTFCN LKYLKLDELT LKKVCGGILP LWKPELISGT REFFVKFMAS IFMWSTRDGH DNNCTFSETC FYVLQMITNW VLDDK LIAL GLTLLHDMQS LLTLDKIFNN ATSNRFSTMA FISSLDILTQ LSKQTKSDYA IQYLIVGPDI MNKVFSSDDP LLLSAA CRY LVATKNKLMQ YPSTNKFVRM QNQYIMDLTN YLYRNKVLSS KSLFGVSPDF FKQILENLYI PTADFKNAKF FTITGIP AL SYICIIILRR LETAENTKIK FTSGIINEET FNNFFRVHHD EIGQHGWIKG VNNIHDLRVK ILMHLSNTAN PYRDIAAF L FTYLKSLSKY SVQNS

UniProtKB: Inner kinetochore subunit CTF3

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Macromolecule #2: Inner kinetochore subunit MCM16

MacromoleculeName: Inner kinetochore subunit MCM16 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.438359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAMTNSSEK QWERIQQLEK EHVEVYRELL ITLDRLYLIR KHNHAVILSH TQQRLLEIRH QLQINLEKTA LLIRLLEKPD NTNVLFTKL QNLLEESNSL DYELLQSLGA QSSLHKQLIE SRAERDELMS KLIELSSKFP KPTIPPDDSD TAGKQVEVEK E NETIQELM IALQIHSGYT NISYTI

UniProtKB: Inner kinetochore subunit MCM16

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Macromolecule #3: Inner kinetochore subunit MCM22

MacromoleculeName: Inner kinetochore subunit MCM22 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.874799 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMDVEKDV LDVYIKNLEN QIGNKRYFLK QAQGAIDEIT KRSLDTEGKP VNSEVFTELL RKPMFFSERA DPIGFSLTSN FLSLRAQSS SEWLSLMNDQ SVDQKAMLLL QNNINSDLKE LLRKLQHQMT IMDSKKQDHA HIRTRKARNK ELWDSLADFL K GYLVPNLD ...String:
SNAMDVEKDV LDVYIKNLEN QIGNKRYFLK QAQGAIDEIT KRSLDTEGKP VNSEVFTELL RKPMFFSERA DPIGFSLTSN FLSLRAQSS SEWLSLMNDQ SVDQKAMLLL QNNINSDLKE LLRKLQHQMT IMDSKKQDHA HIRTRKARNK ELWDSLADFL K GYLVPNLD DNDESIDSLT NEVMLLMKRL IEHDLNLTLN DFSSKTIPIY RLLLRANIIT VIEGSTNPGT KYIKLIDFNE TS LT

UniProtKB: Inner kinetochore subunit MCM22

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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: 8.5
GridModel: C-flat-2/2 / Material: COPPER
VitrificationCryogen name: ETHANE
DetailsRecombinant protein frozen in vitreous ice

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 50.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Details: de novo initial model from a screening dataset (RELION-3.0)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71632
DetailsCounting mode
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6oua:
Cryo-EM structure of the yeast Ctf3 complex

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