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- EMDB-28628: 162bp CX3CR1 nucleosome (further classified with better nucleosom... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | 162bp CX3CR1 nucleosome (further classified with better nucleosome end) | |||||||||
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![]() | nucleosome / transcription factor / transcription / chromatin binding protein-DNA complex / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | ![]() 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 ...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 / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / 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 / 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 / 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 / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / antibacterial humoral response / 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 / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
![]() | Tengfei L / Ruifang G / Yawen B | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of cooperative targeting of the CX3CR1 nucleosome Authors: Tengfei L / Ruifang G / Yawen B | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 26.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
Images | ![]() | 91.8 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 48.9 MB 48.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8evgMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28628_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28628_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : free CX3CR1 nucleosome
Entire | Name: free CX3CR1 nucleosome |
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Components |
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-Supramolecule #1: free CX3CR1 nucleosome
Supramolecule | Name: free CX3CR1 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-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: ![]() |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A type 2-C
Macromolecule | Name: Histone H2A type 2-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.017428 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK UniProtKB: Histone H2A type 2-C |
-Macromolecule #4: Histone H2B type 2-E
Macromolecule | Name: Histone H2B type 2-E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.951239 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK UniProtKB: Histone H2B type 2-E |
-Macromolecule #7: Single-chain variable fragment
Macromolecule | Name: Single-chain variable fragment / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.030146 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...String: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA |
-Macromolecule #5: DNA (162-MER)
Macromolecule | Name: DNA (162-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.043855 KDa |
Sequence | String: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA) ...String: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA)(DG)(DT) (DT)(DG)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DG) (DC)(DT) (DG)(DA)(DG)(DT)(DC)(DT)(DT) (DA)(DG)(DC)(DA)(DA)(DT)(DG)(DG)(DA)(DT) (DA)(DC)(DT) (DT)(DC)(DC)(DC)(DG)(DA) (DT)(DT)(DC)(DC)(DC)(DC)(DT)(DC)(DA)(DC) (DA)(DA)(DA)(DA) (DA)(DT)(DA)(DG)(DG) (DT)(DC)(DA)(DG)(DT)(DC)(DT)(DG)(DT)(DC) (DT)(DG)(DG)(DC)(DT) (DA)(DG)(DT)(DT) (DC)(DT)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DC) (DA)(DG)(DA)(DC)(DA)(DC) (DA)(DG)(DG) (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DG)(DG)(DG) (DT)(DT)(DC)(DC)(DT)(DA)(DT) (DT)(DT) |
-Macromolecule #6: DNA (162-MER)
Macromolecule | Name: DNA (162-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.965957 KDa |
Sequence | String: (DA)(DA)(DA)(DT)(DA)(DG)(DG)(DA)(DA)(DC) (DC)(DC)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DC) (DC)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DG) (DC)(DA)(DA)(DG)(DT)(DA)(DC)(DA)(DG)(DA) (DA) (DC)(DT)(DA)(DG)(DC)(DC) ...String: (DA)(DA)(DA)(DT)(DA)(DG)(DG)(DA)(DA)(DC) (DC)(DC)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DC) (DC)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DG) (DC)(DA)(DA)(DG)(DT)(DA)(DC)(DA)(DG)(DA) (DA) (DC)(DT)(DA)(DG)(DC)(DC)(DA)(DG) (DA)(DC)(DA)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DC)(DT) (DA)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DG)(DA)(DG)(DG)(DG)(DG)(DA)(DA)(DT) (DC)(DG)(DG) (DG)(DA)(DA)(DG)(DT)(DA) (DT)(DC)(DC)(DA)(DT)(DT)(DG)(DC)(DT)(DA) (DA)(DG)(DA)(DC) (DT)(DC)(DA)(DG)(DC) (DA)(DA)(DT)(DG)(DC)(DT)(DG)(DC)(DA)(DA) (DC)(DT)(DC)(DT)(DC) (DA)(DG)(DC)(DA) (DA)(DC)(DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA) (DG)(DA)(DT)(DC)(DA)(DG) (DC)(DA)(DG) (DC)(DC)(DG)(DA)(DG)(DA)(DG)(DG)(DC)(DC) (DC)(DT)(DG)(DC)(DA)(DC)(DC) (DT)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46748 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |