+
Open data
-
Basic information
Entry | Database: PDB / ID: 7r5s | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the human CCAN bound to alpha satellite DNA | ||||||||||||
![]() |
| ||||||||||||
![]() | CELL CYCLE / Chromosome / kinetochore / cell division / centromere | ||||||||||||
Function / homology | ![]() FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / centromere complex assembly / kinetochore organization / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / sex differentiation / CENP-A containing chromatin assembly ...FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / centromere complex assembly / kinetochore organization / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / sex differentiation / CENP-A containing chromatin assembly / resolution of meiotic recombination intermediates / chordate embryonic development / negative regulation of epithelial cell apoptotic process / kinetochore assembly / inner kinetochore / replication fork processing / mitotic sister chromatid segregation / chromosome, centromeric region / centriolar satellite / chromosome organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / positive regulation of epithelial cell proliferation / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / NRIF signals cell death from the nucleus / mitotic spindle organization / positive regulation of protein ubiquitination / chromosome segregation / RHO GTPases Activate Formins / Fanconi Anemia Pathway / PKR-mediated signaling / kinetochore / nuclear matrix / Separation of Sister Chromatids / chromosome / actin cytoskeleton / mitotic cell cycle / nuclear body / cell adhesion / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA damage response / chromatin / regulation of DNA-templated transcription / nucleolus / apoptotic process / signal transduction / DNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||||||||
![]() | Yatskevich, S. / Muir, K.W. / Bellini, D. / Zhang, Z. / Yang, J. / Tischer, T. / Predin, M. / Dendooven, T. / McLaughlin, S.H. / Barford, D. | ||||||||||||
Funding support | ![]() ![]()
| ||||||||||||
![]() | ![]() Title: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome. Authors: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford / ![]() Abstract: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 643.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 500.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 14336MC ![]() 7pb4C ![]() 7pb8C ![]() 7piiC ![]() 7pknC ![]() 7r5rC ![]() 7r5vC ![]() 7ywxC ![]() 7yyhC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Centromere protein ... , 15 types, 15 molecules HIKLMNOPQURTWSX
#1: Protein | Mass: 28520.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Protein | Mass: 86820.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 31696.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 39039.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#6: Protein | Mass: 19761.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#7: Protein | Mass: 39609.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#8: Protein | Mass: 33830.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#9: Protein | Mass: 33210.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#10: Protein | Mass: 30648.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#11: Protein | Mass: 47609.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#12: Protein | Mass: 20228.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#13: Protein | Mass: 60502.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#14: Protein | Mass: 10087.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#15: Protein | Mass: 15917.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#16: Protein | Mass: 8972.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA chain , 2 types, 2 molecules Ji
#3: DNA chain | Mass: 16459.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|---|
#17: DNA chain | Mass: 16197.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/HOH.gif)
#18: Water | ChemComp-HOH / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Human CCAN complex with bound alpha-satellite DNA / Type: COMPLEX / Entity ID: #1-#16 / Source: MULTIPLE SOURCES |
---|---|
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123677 / Symmetry type: POINT |