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- EMDB-40563: Focused map for HELLS midloop bound to the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-40563
TitleFocused map for HELLS midloop bound to the nucleosome
Map dataNon-sharpened cryo-EM map after particle subtraction and local refinement
Sample
  • Complex: Focused map for HELLS midloop bound to the nucleosome
    • Protein or peptide: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
Keywordshelicase / chimera / complex / TRANSLOCASE
Biological speciesHomo sapiens (human) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNartey W / Williams GJ
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04327 Canada
CitationJournal: To Be Published
Title: Focused map for HELLS midloop bound to the nucleosome
Authors: Nartey W / Williams GJ
History
DepositionApr 19, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40563.png

Downloads & links

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Map

FileDownload / File: emd_40563.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharpened cryo-EM map after particle subtraction and local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 448 pix.
= 344.96 Å		0.77 Å/pix.
x 448 pix.
= 344.96 Å		0.77 Å/pix.
x 448 pix.
= 344.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042
Minimum - Maximum-0.20473757 - 0.42808414
Average (Standard dev.)-0.00029439776 (±0.007224654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 344.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40563_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Reference map for focused refinement

Fileemd_40563_additional_1.map
AnnotationReference map for focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened cryo-EM map after particle subtraction and local refinement

Fileemd_40563_additional_2.map
AnnotationSharpened cryo-EM map after particle subtraction and local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map A

Fileemd_40563_half_map_1.map
AnnotationUnfiltered half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map B

Fileemd_40563_half_map_2.map
AnnotationUnfiltered half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Focused map for HELLS midloop bound to the nucleosome

EntireName: Focused map for HELLS midloop bound to the nucleosome
Components
  • Complex: Focused map for HELLS midloop bound to the nucleosome
    • Protein or peptide: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera

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Supramolecule #1: Focused map for HELLS midloop bound to the nucleosome

SupramoleculeName: Focused map for HELLS midloop bound to the nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera

MacromoleculeName: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
type: protein_or_peptide / ID: 1
Details: This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag
Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString: SNAMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ...String:
SNAMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ISRSKEDGET INSDLTEEET VIKLQNELCP LLTGGQLKSY QLKGVKWLIS LWQNGLNGIL ADQMGLGKTI QT IGFLSHL KGNGLDGPYL VIAPLSTLSN WFNEIARFTP SINAIIYHGD KNQRDELRRK HMPKTVGPKF PIVITSYEVA MND AKRILR HYPWKYVVID EGHRLKNHKC KLLRELKHLK MDNKLLLTGT PLQNNLSELW SLLNFILPDI FTSHDEFESW FDFS EKNKN EATKEEEEKR RAQVVSKLHG ILRPFILRRM KCDVELSLPR KKEIIMYATM TDHQKKFQEH LVNNTLEAHL GENAI RGIE LSPTGRPKRR TRKSINYSKI DDFPNELEKL ISQIQPEVDR ERAVVEVNIP VEQGWKGKLN NLVIQLRKNC NHPDLL QGQ IDGSYLYPPV EEIVGQCGKF RLLERLLVRL FANNHKVLIF SQWTKLLDIM DYYFSEKGFE VCRIDGSVKL DERRRQI KD FSDEKSSCSI FLLSTRAGGL GINLTAADTC ILYDSDWNPQ MDLQAMDRCH RIGQTKPVHV YRLSTAQSIE TRVLKRAY S KLKLEHVVIG QGQFHQERAK SSTPLEEEDI LALLKEDETA EDKLIQTDIS DADLDRLLDR SDLTITAPGE TQAAEAFPV KGPGWEVVLP SSGGMLSSLN S

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7808 / Average exposure time: 4.95 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 195090
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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