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- EMDB-14375: Structure of the human CCANdeltaT CENP-A alpha-satellite complex -
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Open data
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Basic information
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Title | Structure of the human CCANdeltaT CENP-A alpha-satellite complex | ||||||||||||
![]() | Local resolution filtered map from Relion | ||||||||||||
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![]() | Chromosome / kinetochore / cell division / centromere / CELL CYCLE | ||||||||||||
Function / homology | ![]() positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / centromere complex assembly / kinetochore organization / spindle attachment to meiosis I kinetochore / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / sex differentiation / CENP-A containing chromatin assembly ...positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / centromere complex assembly / kinetochore organization / spindle attachment to meiosis I kinetochore / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / sex differentiation / CENP-A containing chromatin assembly / chordate embryonic development / protein localization to chromosome, centromeric region / negative regulation of epithelial cell apoptotic process / kinetochore assembly / inner kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / chromosome, centromeric region / centriolar satellite / mitotic cytokinesis / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / Packaging Of Telomere Ends / Mitotic Prometaphase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Resolution of Sister Chromatid Cohesion / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / NRIF signals cell death from the nucleus / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / mitotic spindle organization / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / positive regulation of epithelial cell proliferation / chromosome segregation / HDACs deacetylate histones / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / kinetochore / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / actin cytoskeleton / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / HATs acetylate histones / Processing of DNA double-strand break ends / midbody / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 Å | ||||||||||||
![]() | Yatskevich S / Muir KW / Bellini D / Zhang Z / Yang J / Tischer T / Predin M / Dendooven T / McLaughlin SH / Barford D | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 15.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.2 KB 32.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 59.2 KB | ||
Filedesc metadata | ![]() | 9.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 428.4 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yyhMC ![]() 7pb4C ![]() 7pb8C ![]() 7piiC ![]() 7pknC ![]() 7r5rC ![]() 7r5sC ![]() 7r5vC ![]() 7ywxC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Local resolution filtered map from Relion | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.662 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : CCAN-CENP-A inner centromere complex
+Supramolecule #1: CCAN-CENP-A inner centromere complex
+Macromolecule #1: Histone H3-like centromeric protein A
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-C
+Macromolecule #4: Histone H2B type 1-C/E/F/G/I
+Macromolecule #5: Centromere protein H
+Macromolecule #6: Centromere protein I
+Macromolecule #8: Centromere protein K
+Macromolecule #9: Centromere protein L
+Macromolecule #10: Centromere protein M
+Macromolecule #11: Centromere protein N
+Macromolecule #12: Centromere protein O
+Macromolecule #13: Centromere protein P
+Macromolecule #14: Centromere protein Q
+Macromolecule #15: Centromere protein R
+Macromolecule #16: Centromere protein U
+Macromolecule #17: Centromere protein C
+Macromolecule #7: DNA (171-MER)
+Macromolecule #18: DNA (171-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |