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Yorodumi- EMDB-4711: Structure of LSD2/NPAC-linker/nucleosome core particle complex: C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4711 | |||||||||
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Title | Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 4 | |||||||||
Map data | LSD/NPAC(214-225)/nucleosome: class 4 | |||||||||
Sample |
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Biological species | Xenopus laevis (African clawed frog) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.23 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_4711.map.gz | 61.7 MB | EMDB map data format | |
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Header (meta data) | emd-4711-v30.xml emd-4711.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_4711.png | 119.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4711 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4711 | HTTPS FTP |
-Related structure data
Related structure data | 4704C 4705C 4710C 4712C 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_4711.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | LSD/NPAC(214-225)/nucleosome: class 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : LSD2/NPAC(214-225)/nucleosome
Entire | Name: LSD2/NPAC(214-225)/nucleosome |
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Components |
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-Supramolecule #1: LSD2/NPAC(214-225)/nucleosome
Supramolecule | Name: LSD2/NPAC(214-225)/nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all 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 | Experimental: 290 KDa |
-Macromolecule #1: LSD2
Macromolecule | Name: LSD2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: PLGSRKCEKA GCTATCPVCF ASASERCAKN GYTSRWYHLS CGEHFCNECF DHYYRSHKDG YDKYTTWKKI WTSNGKTEPS PKAFMADQQ LPYWVQCTKP ECRKWRQLTK EIQLTPQIAK TYRCGMKPNT AIKPETSDHC SLPEDLRVLE VSNHWWYSML I LPPLLKDS ...String: PLGSRKCEKA GCTATCPVCF ASASERCAKN GYTSRWYHLS CGEHFCNECF DHYYRSHKDG YDKYTTWKKI WTSNGKTEPS PKAFMADQQ LPYWVQCTKP ECRKWRQLTK EIQLTPQIAK TYRCGMKPNT AIKPETSDHC SLPEDLRVLE VSNHWWYSML I LPPLLKDS VAAPLLSAYY PDCVGMSPSC TSTNRAAATG NASPGKLEHS KAALSVHVPG MNRYFQPFYQ PNECGKALCV RP DVMELDE LYEFPEYSRD PTMYLALRNL ILALWYTNCK EALTPQKCIP HIIVRGLVRI RCVQEVERIL YFMTRKGLIN TGV LSVGAD QYLLPKDYHN KSVIIIGAGP AGLAAARQLH NFGIKVTVLE AKDRIGGRVW DDKSFKGVTV GRGAQIVNGC INNP VALMC EQLGISMHKF GERCDLIQEG GRITDPTIDK RMDFHFNALL DVVSEWRKDK TQLQDVPLGE KIEEIYKAFI KESGI QFSE LEGQVLQFHL SNLEYACGSN LHQVSARSWD HNEFFAQFAG DHTLLTPGYS VIIEKLAEGL DIQLKSPVQC IDYSGD EVQ VTTTDGTGYS AQKVLVTVPL ALLQKGAIQF NPPLSEKKMK AINSLGAGII EKIALQFPYR FWDSKVQGAD FFGHVPP SA SKRGLFAVFY DMDPQKKHSV LMSVIAGEAV ASVRTLDDKQ VLQQCMATLR ELFKEQEVPD PTKYFVTRWS TDPWIQMA Y SFVKTGGSGE AYDIIAEDIQ GTVFFAGEAT NRHFPQTVTG AYLSGVREAS KIAAF |
-Macromolecule #2: NPAC
Macromolecule | Name: NPAC / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: DPHFHHFLLS QT |
-Macromolecule #3: H3
Macromolecule | Name: H3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA |
-Macromolecule #4: H4
Macromolecule | Name: H4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRD AVTYTEHAKR KTVTAMDVVY ALKRQGRTLY GFGG |
-Macromolecule #5: H2A
Macromolecule | Name: H2A / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGN AARDNKKTRI IPRHLQLAVR NDEELNKLLG GVTIAQGGVL PNIQSVLLPK K TESAKSAK SK |
-Macromolecule #6: H2B
Macromolecule | Name: H2B / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK |
-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 |