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- EMDB-9802: Nucleosome bound to C-terminal ELYS fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-9802
TitleNucleosome bound to C-terminal ELYS fragment
Map data
SampleNucleosome bound to C-terminal ELYS fragment
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKobayashi W / Takizawa Y / Aihara M / Negishi L / Ishii H / Kurumizaka H
CitationJournal: 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.
DateDeposition: Feb 1, 2019 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 22, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.7
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_9802.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 160 pix.
= 211.2 Å
1.32 Å/pix.
x 160 pix.
= 211.2 Å
1.32 Å/pix.
x 160 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 3.7 / Movie #1: 3.7
Minimum - Maximum-14.577457000000001 - 24.215945999999999
Average (Standard dev.)-0.000000001179911 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-14.57724.216-0.000

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Supplemental data

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Sample components

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Entire Nucleosome bound to C-terminal ELYS fragment

EntireName: Nucleosome bound to C-terminal ELYS fragment / Number of components: 1

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Component #1: protein, Nucleosome bound to C-terminal ELYS fragment

ProteinName: Nucleosome bound to C-terminal ELYS fragment / Recombinant expression: No
SourceSpecies: 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)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.4 e/Å2 / Illumination mode: OTHER
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2408

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81088
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body

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