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Yorodumi- EMDB-14375: Structure of the human CCANdeltaT CENP-A alpha-satellite complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14375 | ||||||||||||
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Title | Structure of the human CCANdeltaT CENP-A alpha-satellite complex | ||||||||||||
Map data | Local resolution filtered map from Relion | ||||||||||||
Sample |
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Function / homology | Function and homology information 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 / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / chromosome, centromeric region / centriolar satellite / mitotic cytokinesis / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / Packaging Of Telomere Ends / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / chromosome segregation / positive regulation of epithelial cell proliferation / 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 / kinetochore / Meiotic recombination / 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 / Separation of Sister Chromatids / structural constituent of chromatin / 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 | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 Å | ||||||||||||
Authors | Yatskevich S / Muir KW / Bellini D / Zhang Z / Yang J / Tischer T / Predin M / Dendooven T / McLaughlin SH / Barford D | ||||||||||||
Funding support | United Kingdom, Germany, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14375.map.gz | 15.5 MB | EMDB map data format | |
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Header (meta data) | emd-14375-v30.xml emd-14375.xml | 31 KB 31 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14375_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_14375.png | 59.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14375 | HTTPS FTP |
-Validation report
Summary document | emd_14375_validation.pdf.gz | 376.2 KB | Display | EMDB validaton report |
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Full document | emd_14375_full_validation.pdf.gz | 375.8 KB | Display | |
Data in XML | emd_14375_validation.xml.gz | 10 KB | Display | |
Data in CIF | emd_14375_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14375 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14375 | 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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14375.map.gz / Format: CCP4 / Size: 25.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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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 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |