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- PDB-7l7q: Ctf3c with Ulp2-KIM -

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Basic information

Entry
Database: PDB / ID: 7l7q
TitleCtf3c with Ulp2-KIM
Components
  • Inner kinetochore subunit CTF3
  • Inner kinetochore subunit MCM16
  • Inner kinetochore subunit MCM22
KeywordsCELL CYCLE / kinetochore / 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
Inner kinetochore subunit MCM22 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit CTF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHinshaw, S.M. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionDec 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
H: Inner kinetochore subunit MCM16
I: Inner kinetochore subunit CTF3
K: Inner kinetochore subunit MCM22


Theoretical massNumber of molelcules
Total (without water)133,9313
Polymers133,9313
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Inner kinetochore subunit MCM16 / CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome ...CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome maintenance protein 16


Mass: 21438.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q12262
#2: Protein Inner kinetochore subunit CTF3 / CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / ...CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / Constitutive centromere-associated network protein CTF3


Mass: 84617.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q12748
#3: Protein Inner kinetochore subunit MCM22 / CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome ...CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome maintenance protein 22


Mass: 27874.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P47167
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Single particle reconstruction of the Ctf3c bound to Cnn1-Wip1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96787 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055725
ELECTRON MICROSCOPYf_angle_d0.8997728
ELECTRON MICROSCOPYf_dihedral_angle_d21.6332159
ELECTRON MICROSCOPYf_chiral_restr0.044886
ELECTRON MICROSCOPYf_plane_restr0.004969

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