+Open data
-Basic information
Entry | Database: PDB / ID: 7r5s | ||||||||||||
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Title | Structure of the human CCAN bound to alpha satellite DNA | ||||||||||||
Components |
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Keywords | CELL CYCLE / Chromosome / kinetochore / cell division / centromere | ||||||||||||
Function / homology | Function and homology information positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / FANCM-MHF complex / centromere complex assembly / kinetochore organization / metaphase chromosome alignment / Fanconi anaemia nuclear complex / inner kinetochore / kinetochore binding / sex differentiation ...positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / FANCM-MHF complex / centromere complex assembly / kinetochore organization / metaphase chromosome alignment / Fanconi anaemia nuclear complex / inner kinetochore / 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 / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / NRIF signals cell death from the nucleus / mitotic spindle organization / positive regulation of protein ubiquitination / positive regulation of epithelial cell proliferation / chromosome segregation / RHO GTPases Activate Formins / Fanconi Anemia Pathway / PKR-mediated signaling / kinetochore / nuclear matrix / Separation of Sister Chromatids / actin cytoskeleton / mitotic cell cycle / chromosome / nuclear body / cell adhesion / protein heterodimerization activity / cell division / DNA repair / apoptotic process / DNA damage response / chromatin binding / chromatin / nucleolus / regulation of DNA-templated transcription / signal transduction / DNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||||||||
Authors | Yatskevich, S. / Muir, K.W. / Bellini, D. / Zhang, Z. / Yang, J. / Tischer, T. / Predin, M. / Dendooven, T. / McLaughlin, S.H. / Barford, D. | ||||||||||||
Funding support | United Kingdom, Germany, 3items
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Citation | Journal: Science / Year: 2022 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r5s.cif.gz | 638.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r5s.ent.gz | 509.3 KB | Display | PDB format |
PDBx/mmJSON format | 7r5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/7r5s ftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r5s | HTTPS FTP |
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-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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-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.) Homo sapiens (human) / Gene: CENPH, ICEN35 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H3R5 |
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#2: Protein | Mass: 86820.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI, FSHPRH1, ICEN19, LRPR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92674 |
#4: Protein | Mass: 31696.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPK, ICEN37, FKSG14 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BS16 |
#5: Protein | Mass: 39039.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPL, C1orf155, ICEN33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N0S6 |
#6: Protein | Mass: 19761.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM, C22orf18, ICEN39, PANE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NSP4 |
#7: Protein | Mass: 39609.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPN, C16orf60, ICEN32, BM-309 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96H22 |
#8: Protein | Mass: 33830.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO, ICEN36, MCM21R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BU64 |
#9: Protein | Mass: 33210.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6IPU0 |
#10: Protein | Mass: 30648.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPQ, C6orf139 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7L2Z9 |
#11: Protein | Mass: 47609.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q71F23 |
#12: Protein | Mass: 20228.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3BP, CENPR, NRIF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13352 |
#13: Protein | Mass: 60502.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPT, C16orf56, ICEN22 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96BT3 |
#14: Protein | Mass: 10087.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPW, C6orf173, CUG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EE01 |
#15: Protein | Mass: 15917.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPS, APITD1, FAAP16, MHF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N2Z9 |
#16: Protein | Mass: 8972.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPX, FAAP10, MHF2, STRA13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8MT69 |
-DNA chain , 2 types, 2 molecules Ji
#3: DNA chain | Mass: 16459.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 36349 |
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#17: DNA chain | Mass: 16197.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 36349 |
-Non-polymers , 1 types, 1 molecules
#18: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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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 |
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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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
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3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123677 / Symmetry type: POINT |