[English] 日本語
Yorodumi
- EMDB-40562: Focused map for DDM1 motor bound to the nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40562
TitleFocused map for DDM1 motor bound to the nucleosome
Map dataSharpened cryo-EM map after particle subtraction and local refinement
Sample
  • Complex: Focused map for DDM1 motor bound to the nucleosome
    • Protein or peptide: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
Keywordshelicase / chimera / complex / TRANSLOCASE
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 DDM1 motor 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

-
Structure visualization

Supplemental images

emd_40562.png

Downloads & links

-
Map

FileDownload / File: emd_40562.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened 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: 0.08
Minimum - Maximum-0.38503852 - 0.61755157
Average (Standard dev.)-0.00021311357 (±0.008600849)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_40562_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-sharpened cryo-EM map after particle subtraction and local...

Fileemd_40562_additional_1.map
AnnotationNon-sharpened cryo-EM map after particle subtraction and local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Reference map for focused refinement

Fileemd_40562_additional_2.map
AnnotationReference map for focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half-map A

Fileemd_40562_half_map_1.map
AnnotationUnfiltered half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half-map B

Fileemd_40562_half_map_2.map
AnnotationUnfiltered half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Focused map for DDM1 motor bound to the nucleosome

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

-
Supramolecule #1: Focused map for DDM1 motor bound to the nucleosome

SupramoleculeName: Focused map for DDM1 motor bound to the nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
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)
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
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

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more