+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33666 | ||||||||||||||||||||||||
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Title | chicken KNL2 in complex with the CENP-A nucleosome | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | centromere / kinetochore / NUCLEAR PROTEIN-DNA COMPLEX | ||||||||||||||||||||||||
Function / homology | Function and homology information CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes ...CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / 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 / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Gallus gallus (chicken) / Homo sapiens (human) / synthetic construct (others) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||||||||||||||||||||
Authors | Ariyoshi M / Jiang H / Makino F / Fukagawa T | ||||||||||||||||||||||||
Funding support | Japan, 7 items
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Citation | Journal: Biorxiv / Year: 2022 Title: The cryo-EM structure of the CENP-A nucleosome in complex with ggKNL2. Authors: Jiang H / Ariyoshi M / Watanabe R / Makino F / Namba K / Fukagawa T | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33666.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-33666-v30.xml emd-33666.xml | 29.4 KB 29.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33666_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_33666.png | 59.9 KB | ||
Filedesc metadata | emd-33666.cif.gz | 7.5 KB | ||
Others | emd_33666_half_map_1.map.gz emd_33666_half_map_2.map.gz | 19.8 MB 19.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33666 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33666 | HTTPS FTP |
-Validation report
Summary document | emd_33666_validation.pdf.gz | 915.5 KB | Display | EMDB validaton report |
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Full document | emd_33666_full_validation.pdf.gz | 915.1 KB | Display | |
Data in XML | emd_33666_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_33666_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33666 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33666 | HTTPS FTP |
-Related structure data
Related structure data | 7y7iMC 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_33666.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.98 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33666_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33666_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : the CENP-C like motif of chicken KNL2 in complex with the CENP-A ...
+Supramolecule #1: the CENP-C like motif of chicken KNL2 in complex with the CENP-A ...
+Supramolecule #2: chimeric CENP-A
+Supramolecule #3: nucleosome
+Supramolecule #4: DNA
+Supramolecule #5: Myb-like domain-containing protein
+Macromolecule #1: Histone H3.1,Histone H3-like centromeric protein A
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 1-J
+Macromolecule #7: Myb-like domain-containing protein
+Macromolecule #5: Chains: I
+Macromolecule #6: Chains: J
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5858 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 9450 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated magnification: 49000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | Initial local fitting and refinement were performed using PHENIX. The complex model was iteratively modified in Coot and refined in PHENIX. | ||||||
Refinement | Space: REAL / Protocol: OTHER | ||||||
Output model | PDB-7y7i: |