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Yorodumi- EMDB-26330: Cryo-EM structure of CENP-A nucleosome (palindromic alpha satelli... -
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-Basic information
Entry | Database: EMDB / ID: EMD-26330 | |||||||||
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Title | Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nucleosome / CENP-A / kinetochore / CENP-N / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / inner kinetochore / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin ...CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / inner kinetochore / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Replacement of protamines by nucleosomes in the male pronucleus / pericentric heterochromatin / CENP-A containing nucleosome / 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 / Inhibition of DNA recombination at telomere / Resolution of Sister Chromatid Cohesion / telomere organization / Meiotic synapsis / RNA Polymerase I Promoter Opening / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / chromosome segregation / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / antibacterial humoral response / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / negative regulation of cell population proliferation / Amyloid fiber formation / chromatin binding / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | |||||||||
Authors | Zhou K / Luger K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: CENP-N promotes the compaction of centromeric chromatin. Authors: Keda Zhou / Magdalena Gebala / Dustin Woods / Kousik Sundararajan / Garrett Edwards / Dan Krzizike / Jeff Wereszczynski / Aaron F Straight / Karolin Luger / Abstract: The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How ...The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown. Here we demonstrate that the human CENP-A-interacting protein CENP-N promotes the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays through a previously undefined interaction between the α6 helix of CENP-N with the DNA of a neighboring nucleosome. We describe the cryo-EM structures and biophysical characterization of such CENP-N-mediated nucleosome stacks and nucleosomal arrays and demonstrate that this interaction is responsible for the formation of densely packed chromatin at the centromere in the cell. Our results provide first evidence that CENP-A, together with CENP-N, promotes specific chromatin higher order structure at the centromere. | |||||||||
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_26330.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-26330-v30.xml emd-26330.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26330_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_26330.png | 30.4 KB | ||
Masks | emd_26330_msk_1.map | 163.6 MB | Mask map | |
Filedesc metadata | emd-26330.cif.gz | 6.5 KB | ||
Others | emd_26330_half_map_1.map.gz emd_26330_half_map_2.map.gz | 151.6 MB 151.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26330 | HTTPS FTP |
-Validation report
Summary document | emd_26330_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_26330_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_26330_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_26330_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26330 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26330 | HTTPS FTP |
-Related structure data
Related structure data | 7u46MC 7u47C 7u4dC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_26330.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8211 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_26330_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26330_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26330_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CENP-A nucleosome with kinetochore protein CENP-N
Entire | Name: CENP-A nucleosome with kinetochore protein CENP-N |
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Components |
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-Supramolecule #1: CENP-A nucleosome with kinetochore protein CENP-N
Supramolecule | Name: CENP-A nucleosome with kinetochore protein CENP-N / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Histone H3-like centromeric protein A
Macromolecule | Name: Histone H3-like centromeric protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.02363 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV TLFPKDVQLA RRIRGLEEGL G UniProtKB: Histone H3-like centromeric protein A |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.135523 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A type 1-C |
-Macromolecule #4: Histone H2B type 1-C/E/F/G/I
Macromolecule | Name: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.937213 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK UniProtKB: Histone H2B type 1-C/E/F/G/I |
-Macromolecule #5: Centromere protein N
Macromolecule | Name: Centromere protein N / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.870695 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWDVFQMS KGPGEDVDLF DMKQFKNSFK KILQRALKNV TVSFRETEEN AVWIRIAWGT QYTKPNQYKP TYVVYYSQTP Y AFTSSSML ...String: MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWDVFQMS KGPGEDVDLF DMKQFKNSFK KILQRALKNV TVSFRETEEN AVWIRIAWGT QYTKPNQYKP TYVVYYSQTP Y AFTSSSML RRNTPLLGQA LTIASKHHQI VKMDLRSRYL DSLKAIVFKQ YNQTFETHNS TTPLQERSLG LDINMDSRII HE NIVEKER VQRITQETFG DYPQPQLEFA QYKLETKFKS GLNGSILAER EEHHHHHH UniProtKB: Centromere protein N |
-Macromolecule #6: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 45.368051 KDa |
Sequence | String: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DA)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DA)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DA)(DA)(DT)(DC)(DC) (DA)(DG)(DC) (DT)(DG)(DA)(DA)(DC)(DA) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA) (DT)(DG)(DG)(DA) (DG)(DC)(DA)(DG)(DT) (DT)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC) (DA)(DC)(DT)(DT)(DT) (DT)(DG)(DG)(DT) (DA)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DC)(DA) (DG)(DG)(DT)(DG)(DG)(DA) (DT)(DA)(DT) (DT)(DG)(DA)(DT) |
-Macromolecule #7: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 45.359035 KDa |
Sequence | String: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DA)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DA)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DA)(DT)(DT)(DC)(DC) (DA)(DG)(DC) (DT)(DG)(DA)(DA)(DC)(DA) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA) (DT)(DG)(DG)(DA) (DG)(DC)(DA)(DG)(DT) (DT)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC) (DA)(DC)(DT)(DT)(DT) (DT)(DG)(DG)(DT) (DA)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DC)(DA) (DG)(DG)(DT)(DG)(DG)(DA) (DT)(DA)(DT) (DT)(DG)(DA)(DT) |
-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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Grid | Model: C-flat / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
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: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |