+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Nucleosome 2 of the 4x177 nucleosome array containing H1 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Chromatin / Nucleosomes / Linker Histone / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends ...negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / heterochromatin / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / arachidonate metabolic process / Chromatin modifying enzymes / 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 / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / 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 / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / euchromatin / heterochromatin formation / chromatin DNA binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / double-stranded DNA binding / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | |||||||||
![]() | Dombrowski M / Cramer P | |||||||||
Funding support | European Union, 1 items
| |||||||||
![]() | ![]() Title: Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Authors: Marco Dombrowski / Maik Engeholm / Christian Dienemann / Svetlana Dodonova / Patrick Cramer / ![]() Abstract: Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM ...Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.5 KB 16.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 62.4 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pexMC ![]() 7petC ![]() 7peuC ![]() 7pevC ![]() 7pewC ![]() 7peyC ![]() 7pezC ![]() 7pf0C ![]() 7pf2C ![]() 7pf3C ![]() 7pf4C ![]() 7pf5C ![]() 7pf6C ![]() 7pfaC ![]() 7pfcC ![]() 7pfdC ![]() 7pfeC ![]() 7pffC ![]() 7pftC ![]() 7pfuC ![]() 7pfvC ![]() 7pfwC ![]() 7pfxC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
-Entire : Nucleosome 2 from 4x177 nucleosome array
Entire | Name: Nucleosome 2 from 4x177 nucleosome array |
---|---|
Components |
|
-Supramolecule #1: Nucleosome 2 from 4x177 nucleosome array
Supramolecule | Name: Nucleosome 2 from 4x177 nucleosome array / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|
-Macromolecule #1: Histone H3.2
Macromolecule | Name: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.389036 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.2 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
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: Arachidonate 15-lipoxygenase |
-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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.344873 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: HHHHHHENLY FQSNAPWMSG RGKQGGKARA KAKTRSSRAG LQFPVGRVHR LLRKGNYSER VGAGAPVYLA AVLEYLTAEI LELAGNAAR DNKKTRIIPR HLQLAIRNDE ELNKLLGRVT IAQGGVLPNI QAVLLPKKTE SHHKAKGK UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #4: Histone H2B type 1-K
Macromolecule | Name: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.921213 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-K |
-Macromolecule #7: Histone H1.4
Macromolecule | Name: Histone H1.4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 21.800326 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SETAPAAPAA PAPAEKTPVK KKARKSAGAA KRKASGPPVS ELITKAVAAS KERSGVSLAA LKKALAAAGY DVEKNNSRIK LGLKSLVSK GTLVQTKGTG ASGSFKLNKK AASGEAKPKA KKAGAAKAKK PAGAAKKPKK ATGAATPKKS AKKTPKKAKK P AAAAGAKK ...String: SETAPAAPAA PAPAEKTPVK KKARKSAGAA KRKASGPPVS ELITKAVAAS KERSGVSLAA LKKALAAAGY DVEKNNSRIK LGLKSLVSK GTLVQTKGTG ASGSFKLNKK AASGEAKPKA KKAGAAKAKK PAGAAKKPKK ATGAATPKKS AKKTPKKAKK P AAAAGAKK AKSPKKAKAA KPKKAPKSPA KAKAVKPKAA KPKTAKPKAA KPKKAAAKKK UniProtKB: Histone H1.4 |
-Macromolecule #5: DNA (177-MER)
Macromolecule | Name: DNA (177-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 55.011 KDa |
Sequence | String: (DG)(DG)(DG)(DT)(DC)(DC)(DG)(DG)(DC)(DA) (DC)(DT)(DG)(DG)(DA)(DA)(DC)(DA)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DG)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG) (DC)(DC)(DT)(DG)(DG)(DA) ...String: (DG)(DG)(DG)(DT)(DC)(DC)(DG)(DG)(DC)(DA) (DC)(DT)(DG)(DG)(DA)(DA)(DC)(DA)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DG)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC) (DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG) (DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT)(DC)(DC) (DA)(DG) (DG)(DG)(DG)(DA)(DT)(DC)(DC)(DG)(DG)(DA) (DT)(DG)(DC)(DT)(DC) |
-Macromolecule #6: DNA (177-MER)
Macromolecule | Name: DNA (177-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 54.281535 KDa |
Sequence | String: (DG)(DA)(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DG) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DG)(DG)(DA) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG) (DC)(DT)(DC)(DA)(DA)(DT) ...String: (DG)(DA)(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DG) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DG)(DG)(DA) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG) (DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC) (DG)(DC)(DA) (DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC) (DG)(DT)(DG) (DT)(DC)(DA)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA)(DT)(DC)(DC)(DT) (DG)(DT) (DT)(DC)(DC)(DA)(DG)(DT)(DG)(DC)(DC)(DG) (DG)(DA)(DC)(DC)(DC) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.1 mg/mL |
---|---|
Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |