+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14351 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the human CCAN CENP-A alpha-satellite complex | ||||||||||||
Map data | Local resolution filtered cryosparc homogeneous refinement map | ||||||||||||
Sample |
| ||||||||||||
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 / spindle attachment to meiosis I kinetochore / Fanconi anaemia nuclear complex / inner kinetochore / kinetochore binding ...positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / FANCM-MHF complex / centromere complex assembly / kinetochore organization / metaphase chromosome alignment / spindle attachment to meiosis I kinetochore / Fanconi anaemia nuclear complex / inner kinetochore / kinetochore binding / centromeric DNA binding / sex differentiation / CENP-A containing chromatin assembly / resolution of meiotic recombination intermediates / chordate embryonic development / protein localization to chromosome, centromeric region / negative regulation of epithelial cell apoptotic process / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / replication fork processing / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / centriolar satellite / chromosome organization / 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 / interstrand cross-link repair / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / 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 / Resolution of Sister Chromatid Cohesion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / NRIF signals cell death from the nucleus / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / mitotic spindle organization / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / positive regulation of protein ubiquitination / Defective pyroptosis / positive regulation of epithelial cell proliferation / chromosome segregation / RHO GTPases Activate Formins / HDACs deacetylate histones / Fanconi Anemia Pathway / 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 / PKR-mediated signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / kinetochore / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / 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 / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 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
| ||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_14351.map.gz | 11.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-14351-v30.xml emd-14351.xml | 35.6 KB 35.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14351_fsc.xml | 6.2 KB | Display | FSC data file |
Images | emd_14351.png | 39.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14351 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14351 | HTTPS FTP |
-Related structure data
Related structure data | 7ywxMC 7pb4C 7pb8C 7piiC 7pknC 7r5rC 7r5sC 7r5vC 7yyhC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_14351.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Local resolution filtered cryosparc homogeneous refinement map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
+Entire : CCAN-CENP-A inner centromere complex
+Supramolecule #1: CCAN-CENP-A inner centromere complex
+Macromolecule #1: Centromere protein H
+Macromolecule #2: Centromere protein I
+Macromolecule #3: Centromere protein K
+Macromolecule #4: Centromere protein L
+Macromolecule #5: Centromere protein M
+Macromolecule #6: Centromere protein N
+Macromolecule #7: Centromere protein O
+Macromolecule #8: Centromere protein Q
+Macromolecule #9: Centromere protein U
+Macromolecule #10: Centromere protein P
+Macromolecule #11: Centromere protein R
+Macromolecule #12: Centromere protein T
+Macromolecule #13: Centromere protein W
+Macromolecule #14: Centromere protein S
+Macromolecule #15: Centromere protein X
+Macromolecule #18: Histone H3-like centromeric protein A
+Macromolecule #19: Histone H4
+Macromolecule #20: Histone H2A type 1-C
+Macromolecule #21: Histone H2B type 1-C/E/F/G/I
+Macromolecule #22: Centromere protein C
+Macromolecule #16: DNA (171-MER)
+Macromolecule #17: DNA (171-MER)
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |