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Yorodumi- EMDB-4712: Structure of LSD2/NPAC-linker/nucleosome core particle complex: C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4712 | |||||||||
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Title | Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 5 | |||||||||
Map data | Unfolded nucleosome | |||||||||
Sample |
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Biological species | Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.95 Å | |||||||||
Authors | Marabelli C / Pilotto S / Chittori S / Subramaniam S / Mattevi A | |||||||||
Citation | Journal: Cell Rep / Year: 2019 Title: A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex. Authors: Chiara Marabelli / Biagina Marrocco / Simona Pilotto / Sagar Chittori / Sarah Picaud / Sara Marchese / Giuseppe Ciossani / Federico Forneris / Panagis Filippakopoulos / Guy Schoehn / Daniela ...Authors: Chiara Marabelli / Biagina Marrocco / Simona Pilotto / Sagar Chittori / Sarah Picaud / Sara Marchese / Giuseppe Ciossani / Federico Forneris / Panagis Filippakopoulos / Guy Schoehn / Daniela Rhodes / Sriram Subramaniam / Andrea Mattevi / Abstract: LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase ...LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes. | |||||||||
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_4712.map.gz | 62.6 MB | EMDB map data format | |
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Header (meta data) | emd-4712-v30.xml emd-4712.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_4712.png | 92.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4712 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4712 | HTTPS FTP |
-Validation report
Summary document | emd_4712_validation.pdf.gz | 193.5 KB | Display | EMDB validaton report |
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Full document | emd_4712_full_validation.pdf.gz | 192.6 KB | Display | |
Data in XML | emd_4712_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4712 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4712 | HTTPS FTP |
-Related structure data
Related structure data | 4704C 4705C 4710C 4711C 6r1tC 6r1uC 6r25C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4712.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unfolded nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : partly unfolded nucleosome
Entire | Name: partly unfolded nucleosome |
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Components |
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-Supramolecule #1: partly unfolded nucleosome
Supramolecule | Name: partly unfolded nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 Details: Xenopus laevis histones recombinantly expressed. Alkylated K4C-C110A H3. 601 Widom DNA sequence. Human LSD2 Human NPAC |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 178 KDa |
-Macromolecule #1: H3
Macromolecule | Name: H3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA |
-Macromolecule #2: H4
Macromolecule | Name: H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG |
-Macromolecule #3: H2A
Macromolecule | Name: H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK |
-Macromolecule #4: H2B
Macromolecule | Name: H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVND VFERIAGEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV T KYTSAK |
-Macromolecule #7: H3
Macromolecule | Name: H3 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA |
-Macromolecule #8: H4
Macromolecule | Name: H4 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG |
-Macromolecule #5: DNA (147mer)
Macromolecule | Name: DNA (147mer) / type: dna / ID: 5 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: ATCGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTT AAGCGGTGCT AGAGCTGTCT ACGACCAATT GAGCGGCCTC GGCACCGGGA TTCTCGAT |
-Macromolecule #6: DNA (147mer)
Macromolecule | Name: DNA (147mer) / type: dna / ID: 6 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTT AACCGCCAAG GGGATTACTC CCTAGTCTCC AGGCACGTGT CAGATATATA CATCCGAT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.87 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE | |||||||||
Details | LSD2/NPAC(214-225)/nucleosome was monodisperse (gel filtration peak isolation and concentration in buffer described. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2078 / Average exposure time: 8.0 sec. / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.00305 µm / Nominal defocus min: 0.0007 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |