+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43193 | |||||||||
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Title | Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv | |||||||||
Map data | Main map | |||||||||
Sample |
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Keywords | nucleosome / pioneer transcription factors / DNA binding proteins / transcription / chromatin / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information 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 / Packaging Of Telomere Ends / epigenetic regulation of gene expression / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...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 / Packaging Of Telomere Ends / epigenetic regulation of gene expression / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate 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 / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / heterochromatin formation / 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 / 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 | Homo sapiens (human) / Mus musculus (house mouse) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Zhou BR / Bai Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol.Cell / Year: 2024 Title: Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Authors: Zhou BR / Bai Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43193.map.gz | 33.2 MB | EMDB map data format | |
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Header (meta data) | emd-43193-v30.xml emd-43193.xml | 24.6 KB 24.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43193_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_43193.png | 166.1 KB | ||
Filedesc metadata | emd-43193.cif.gz | 6.5 KB | ||
Others | emd_43193_additional_1.map.gz emd_43193_additional_2.map.gz emd_43193_half_map_1.map.gz emd_43193_half_map_2.map.gz | 32.5 MB 32.5 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43193 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43193 | HTTPS FTP |
-Validation report
Summary document | emd_43193_validation.pdf.gz | 825.5 KB | Display | EMDB validaton report |
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Full document | emd_43193_full_validation.pdf.gz | 825.1 KB | Display | |
Data in XML | emd_43193_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_43193_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43193 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43193 | HTTPS FTP |
-Related structure data
Related structure data | 8vfxMC 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_43193.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Class 3
File | emd_43193_additional_1.map | ||||||||||||
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Annotation | Class 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Class 2
File | emd_43193_additional_2.map | ||||||||||||
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Annotation | Class 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_43193_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_43193_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 186bp ALBN1 nucleosome in complex with scFv
Entire | Name: 186bp ALBN1 nucleosome in complex with scFv |
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Components |
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-Supramolecule #1: 186bp ALBN1 nucleosome in complex with scFv
Supramolecule | Name: 186bp ALBN1 nucleosome in complex with scFv / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Homo sapiens (human) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / 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: 14.165551 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #4: Histone H2B type 1-J
Macromolecule | Name: Histone H2B type 1-J / 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: 13.935239 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-J |
-Macromolecule #5: scFv
Macromolecule | Name: scFv / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 29.34542 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV ...String: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV KMPCKASGYT FTSYTIQWVK QTPRQGLEWI GYIYPYNAGT KYNEKFKGKA TLTSDKSSST VYMELSSLTS ED SAVYYCA RKSSRLRSTL DYWGQGTSVT VSS |
-Macromolecule #6: DNA (158-MER)
Macromolecule | Name: DNA (158-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 57.399637 KDa |
Sequence | String: (DA)(DT)(DC)(DC)(DG)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DG) (DG) (DG)(DC)(DA)(DC)(DT)(DG) ...String: (DA)(DT)(DC)(DC)(DG)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DG) (DG) (DG)(DC)(DA)(DC)(DT)(DG)(DT)(DA) (DC)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DT)(DA) (DC)(DC) (DA)(DG)(DG)(DG)(DA)(DA)(DT) (DG)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DT) (DA)(DA)(DA) (DT)(DA)(DC)(DC)(DA)(DT) (DC)(DA)(DT)(DT)(DC)(DC)(DG)(DG)(DA)(DC) (DG)(DT)(DG)(DT) (DT)(DT)(DG)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DT)(DT) (DT)(DT)(DC)(DC)(DA) (DT)(DG)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DG)(DT)(DT) (DT)(DG)(DG) (DA)(DC)(DT)(DG)(DA)(DT)(DC)(DA)(DA)(DT) (DA)(DC)(DA)(DG)(DT)(DC)(DC) (DT)(DC) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DC)(DA)(DA)(DT)(DA)(DG)(DG) (DA) (DA)(DA)(DG)(DA)(DT) |
-Macromolecule #7: DNA (158-MER)
Macromolecule | Name: DNA (158-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 57.42777 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DA) (DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG)(DA) (DC)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT) (DC) (DA)(DG)(DT)(DC)(DC)(DA) ...String: (DA)(DT)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DA) (DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG)(DA) (DC)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT) (DC) (DA)(DG)(DT)(DC)(DC)(DA)(DA)(DA) (DC)(DT)(DT)(DC)(DT)(DT)(DT)(DC)(DT)(DG) (DC)(DA) (DT)(DG)(DT)(DA)(DC)(DA)(DT) (DG)(DG)(DA)(DA)(DA)(DA)(DC)(DT)(DG)(DG) (DC)(DC)(DA) (DA)(DG)(DG)(DC)(DA)(DA) (DA)(DC)(DA)(DC)(DG)(DT)(DC)(DC)(DG)(DG) (DA)(DA)(DT)(DG) (DA)(DT)(DG)(DG)(DT) (DA)(DT)(DT)(DT)(DA)(DA)(DG)(DA)(DA)(DC) (DA)(DA)(DA)(DC)(DA) (DT)(DT)(DC)(DC) (DC)(DT)(DG)(DG)(DT)(DA)(DT)(DC)(DA)(DG) (DC)(DA)(DA)(DG)(DT)(DA) (DC)(DA)(DG) (DT)(DG)(DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG) (DA)(DC)(DA)(DG)(DA)(DG)(DC) (DA)(DG) (DG)(DA)(DG)(DA)(DC)(DA)(DC)(DA)(DA)(DA) (DG)(DT)(DA)(DC)(DC)(DA)(DT)(DC) (DT) (DC)(DG)(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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |