|Entry||Database: EMDB / ID: EMD-9802|
|Title||Nucleosome bound to C-terminal ELYS fragment|
|Sample||Nucleosome bound to C-terminal ELYS fragment|
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.3 Å|
|Authors||Kobayashi W / Takizawa Y / Aihara M / Negishi L / Ishii H / Kurumizaka H|
|Citation||Journal: Commun Biol / Year: 2019|
Title: Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding.
Authors: Wataru Kobayashi / Yoshimasa Takizawa / Maya Aihara / Lumi Negishi / Hajime Ishii / Hitoshi Kurumizaka /
Abstract: The nuclear pore complex embedded within the nuclear envelope is the essential architecture for trafficking macromolecules, such as proteins and RNAs, between the cytoplasm and nucleus. The nuclear ...The nuclear pore complex embedded within the nuclear envelope is the essential architecture for trafficking macromolecules, such as proteins and RNAs, between the cytoplasm and nucleus. The nuclear pore complex assembly occurs on chromatin in the post-mitotic phase of the cell cycle. ELYS (MEL-28/AHCTF1) binds to the nucleosome, which is the basic chromatin unit, and promotes assembly of the complex around the chromosomes in cells. Here we show that the Arg-Arg-Lys (RRK) stretch of the C-terminal ELYS region plays an essential role in the nucleosome binding. The cryo-EM structure and the crosslinking mass spectrometry reveal that the ELYS C-terminal region directly binds to the acidic patch of the nucleosome. These results provide mechanistic insight into the ELYS-nucleosome interaction, which promotes the post-mitotic nuclear pore complex formation around chromosomes in cells.
|Date||Deposition: Feb 1, 2019 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 22, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_9802.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.32 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Nucleosome bound to C-terminal ELYS fragment
|Entire||Name: Nucleosome bound to C-terminal ELYS fragment / Number of components: 1|
-Component #1: protein, Nucleosome bound to C-terminal ELYS fragment
|Protein||Name: Nucleosome bound to C-terminal ELYS fragment / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
Vector: pGEX6P-1-xELYS(2299-2408), pET15b-H3.1, pET15b-H4, pET15b-H2A, pET15b-H2B, pGEM-T-Easy-(Widom 601 145 base-pair)
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Imaging||Microscope: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.4 e/Å2 / Illumination mode: OTHER|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Image acquisition||Number of digital images: 2408|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81088|
|3D reconstruction||Software: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body|
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