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- EMDB-25180: SMARCAD1-nucleosome map 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-25180
TitleSMARCAD1-nucleosome map 1
Map data
Sample
  • Complex: SMARCAD1-nucleosome
    • Complex: SMARCAD1
    • Complex: nucleosome histones
    • Complex: nucleosome DNA
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.49 Å
AuthorsMarkert J / Luger K
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2021
Title: SMARCAD1 is an ATP-dependent histone octamer exchange factor with de novo nucleosome assembly activity.
Authors: Jonathan Markert / Keda Zhou / Karolin Luger /
Abstract: The adenosine 5′-triphosphate (ATP)–dependent chromatin remodeler SMARCAD1 acts on nucleosomes during DNA replication, repair, and transcription, but despite its implication in disease, ...The adenosine 5′-triphosphate (ATP)–dependent chromatin remodeler SMARCAD1 acts on nucleosomes during DNA replication, repair, and transcription, but despite its implication in disease, information on its function and biochemical activities is scarce. Chromatin remodelers use the energy of ATP hydrolysis to slide nucleosomes, evict histones, or exchange histone variants. Here, we show that SMARCAD1 transfers the entire histone octamer from one DNA segment to another in an ATP-dependent manner but is also capable of de novo nucleosome assembly from histone octamer because of its ability to simultaneously bind all histones. We present a low-resolution cryo–electron microscopy structure of SMARCAD1 in complex with a nucleosome and show that the adenosine triphosphatase domains engage their substrate unlike any other chromatin remodeler. Our biochemical and structural data provide mechanistic insights into SMARCAD1-induced nucleosome disassembly and reassembly.
History
DepositionOct 20, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00114
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00114
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25180.png

Downloads & links

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Map

FileDownload / File: emd_25180.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 272.64 Å		1.07 Å/pix.
x 256 pix.
= 272.64 Å		1.07 Å/pix.
x 256 pix.
= 272.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00114 / Movie #1: 0.00114
Minimum - Maximum-0.0035291568 - 0.0120863225
Average (Standard dev.)-5.0041202e-05 (±0.0006217021)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.640272.640272.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0040.012-0.000

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Supplemental data

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Sample components

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Entire : SMARCAD1-nucleosome

EntireName: SMARCAD1-nucleosome
Components
  • Complex: SMARCAD1-nucleosome
    • Complex: SMARCAD1
    • Complex: nucleosome histones
    • Complex: nucleosome DNA

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Supramolecule #1: SMARCAD1-nucleosome

SupramoleculeName: SMARCAD1-nucleosome / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: SMARCAD1

SupramoleculeName: SMARCAD1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: nucleosome histones

SupramoleculeName: nucleosome histones / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: nucleosome DNA

SupramoleculeName: nucleosome DNA / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20135
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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