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Yorodumi- EMDB-9252: CENP-A nucleosome bound by two copies of CENP-C(CD) and two copie... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9252 | |||||||||
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Title | CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) with local refinement | |||||||||
Map data | CENP-A nucleosome bound by two copies of CENP-CCD and two copies CENP-NNT with local refinement, primary map | |||||||||
Sample |
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Function / homology | Function and homology information spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / protein localization to CENP-A containing chromatin ...spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / mitotic cytokinesis / chromosome, centromeric region / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / arachidonate metabolic process / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / Resolution of Sister Chromatid Cohesion / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / chromosome segregation / RNA Polymerase I Promoter Escape / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / 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 / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / kinetochore / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / HATs acetylate histones / midbody / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nuclear body / Ub-specific processing proteases / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of cell population proliferation / chromatin binding / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Allu PK / Black BE | |||||||||
Citation | Journal: Curr Biol / Year: 2019 Title: Structure of the Human Core Centromeric Nucleosome Complex. Authors: Praveen Kumar Allu / Jennine M Dawicki-McKenna / Trevor Van Eeuwen / Moriya Slavin / Merav Braitbard / Chen Xu / Nir Kalisman / Kenji Murakami / Ben E Black / Abstract: Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the ...Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the histone H3 variant, CENP-A, and its binding proteins, CENP-C (through its central domain; CD) and CENP-N (through its N-terminal domain; NT). CENP-C can engage nucleosomes through two domains: the CD and the CENP-C motif (CM). CENP-C is part of the CCNC by virtue of its high specificity for CENP-A nucleosomes and ability to stabilize CENP-A at the centromere. CENP-C is thought to engage a neighboring nucleosome, either one containing conventional H3 or CENP-A, and a crystal structure of a nucleosome complex containing two copies of CENP-C was reported. Recent structures containing a single copy of CENP-N bound to the CENP-A nucleosome in the absence of CENP-C were reported. Here, we find that one copy of CENP-N is lost for every two copies of CENP-C on centromeric chromatin just prior to kinetochore formation. We present the structures of symmetric and asymmetric forms of the CCNC that vary in CENP-N stoichiometry. Our structures explain how the central domain of CENP-C achieves its high specificity for CENP-A nucleosomes and how CENP-C and CENP-N sandwich the histone H4 tail. The natural centromeric DNA path in our structures corresponds to symmetric surfaces for CCNC assembly, deviating from what is observed in prior structures using artificial sequences. At mitosis, we propose that CCNC asymmetry accommodates its asymmetric connections at the chromosome/kinetochore interface. VIDEO ABSTRACT. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9252.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-9252-v30.xml emd-9252.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9252_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_9252.png | 193.8 KB | ||
Others | emd_9252_additional.map.gz | 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9252 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9252 | HTTPS FTP |
-Validation report
Summary document | emd_9252_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_9252_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_9252_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9252 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9252 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9252.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CENP-A nucleosome bound by two copies of CENP-CCD and two copies CENP-NNT with local refinement, primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: CENP-A nucleosome bound by two copies of CENP-CCD...
File | emd_9252_additional.map | ||||||||||||
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Annotation | CENP-A nucleosome bound by two copies of CENP-CCD and two copies CENP-NNT with local refinement, additional map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : chromatin complex
Entire | Name: chromatin complex |
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Components |
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-Supramolecule #1: chromatin complex
Supramolecule | Name: chromatin complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 276 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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