+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23216 | |||||||||
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Title | Ctf3c with Ulp2-KIM | |||||||||
Map data | Ctf3c with Ulp2-KIM peptide | |||||||||
Sample |
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Keywords | kinetochore / cell cycle / sumo / DNA / chromosome segregation | |||||||||
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 | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Hinshaw SM / Harrison SC | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Cell Biol / Year: 2021 Title: Ctf3/CENP-I provides a docking site for the desumoylase Ulp2 at the kinetochore. Authors: Yun Quan / Stephen M Hinshaw / Pang-Che Wang / Stephen C Harrison / Huilin Zhou / Abstract: The step-by-step process of chromosome segregation defines the stages of the cell cycle. In eukaryotes, signals controlling these steps converge upon the kinetochore, a multiprotein assembly that ...The step-by-step process of chromosome segregation defines the stages of the cell cycle. In eukaryotes, signals controlling these steps converge upon the kinetochore, a multiprotein assembly that connects spindle microtubules to chromosomal centromeres. Kinetochores control and adapt to major chromosomal transactions, including replication of centromeric DNA, biorientation of sister centromeres on the metaphase spindle, and transit of sister chromatids into daughter cells during anaphase. Although the mechanisms that ensure tight microtubule coupling at anaphase are at least partly understood, kinetochore adaptations that support other cell cycle transitions are not. We report here a mechanism that enables regulated control of kinetochore sumoylation. A conserved surface of the Ctf3/CENP-I kinetochore protein provides a binding site for Ulp2, the nuclear enzyme that removes SUMO chains from modified substrates. Ctf3 mutations that disable Ulp2 recruitment cause elevated inner kinetochore sumoylation and defective chromosome segregation. The location of the site within the assembled kinetochore suggests coordination between sumoylation and other cell cycle-regulated processes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23216.map.gz | 65.4 MB | EMDB map data format | |
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Header (meta data) | emd-23216-v30.xml emd-23216.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_23216.png | 114 KB | ||
Masks | emd_23216_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-23216.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23216 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23216 | HTTPS FTP |
-Validation report
Summary document | emd_23216_validation.pdf.gz | 502.4 KB | Display | EMDB validaton report |
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Full document | emd_23216_full_validation.pdf.gz | 501.9 KB | Display | |
Data in XML | emd_23216_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_23216_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23216 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23216 | HTTPS FTP |
-Related structure data
Related structure data | 7l7qMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23216.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ctf3c with Ulp2-KIM peptide | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23216_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Single particle reconstruction of the Ctf3c bound to Cnn1-Wip1
Entire | Name: Single particle reconstruction of the Ctf3c bound to Cnn1-Wip1 |
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Components |
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-Supramolecule #1: Single particle reconstruction of the Ctf3c bound to Cnn1-Wip1
Supramolecule | Name: Single particle reconstruction of the Ctf3c bound to Cnn1-Wip1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Inner kinetochore subunit MCM16
Macromolecule | Name: Inner kinetochore subunit MCM16 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 21.438359 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Inner kinetochore subunit CTF3
Macromolecule | Name: Inner kinetochore subunit CTF3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 84.617891 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #3: Inner kinetochore subunit MCM22
Macromolecule | Name: Inner kinetochore subunit MCM22 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 27.874799 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.4 sec. / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 96787 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |