[English] 日本語
Yorodumi
- EMDB-31805: Negative-staining map of T4 DNA ligase-AMP-DNA Ternary Complex I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31805
TitleNegative-staining map of T4 DNA ligase-AMP-DNA Ternary Complex I
Map dataT4 DNA ligase binding nick double-stranded DNA complex conformation Straight I
Sample
  • Complex: T4 DNA ligase binding nick double-stranded DNA complex conformation Straight I
KeywordsLigase / Complex / DNA Repair / DNA replication / DNA BINDING PROTEIN
Biological speciesbacteriophage T (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 13.4 Å
AuthorsZhang L / Li N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11922410 China
CitationJournal: To Be Published
Title: Repair of DNA nick by T4 DNA ligase in three parallel pathways
Authors: Zhang L / Li N
History
DepositionAug 23, 2021-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31805.png

Downloads & links

-
Map

FileDownload / File: emd_31805.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT4 DNA ligase binding nick double-stranded DNA complex conformation Straight I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 100 pix.
= 160.7 Å		1.61 Å/pix.
x 100 pix.
= 160.7 Å		1.61 Å/pix.
x 100 pix.
= 160.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.607 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0317
Minimum - Maximum-0.00000064851565 - 0.21774095
Average (Standard dev.)0.007555946 (±0.028990574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 160.7 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : T4 DNA ligase binding nick double-stranded DNA complex conformati...

EntireName: T4 DNA ligase binding nick double-stranded DNA complex conformation Straight I
Components
  • Complex: T4 DNA ligase binding nick double-stranded DNA complex conformation Straight I

-
Supramolecule #1: T4 DNA ligase binding nick double-stranded DNA complex conformati...

SupramoleculeName: T4 DNA ligase binding nick double-stranded DNA complex conformation Straight I
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: bacteriophage T (virus)
Molecular weightTheoretical: 55 KDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.011 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
10.0 mMMgCl2Magnesium chloride
10.0 mMDTTDithiothreitol
0.3 mMATPadenosine-triphosphate
50.0 mMTris-HClTris(Hydroxymethyl)aminomethane
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: A 4.0 uL drop of the sample was placed on a glow-discharged EM specimen grid (CF200-Cu, Electron Microscopy Sciences, Hatfield, PA, USA) with a thin carbon film for 1 min and the excess ...Details: A 4.0 uL drop of the sample was placed on a glow-discharged EM specimen grid (CF200-Cu, Electron Microscopy Sciences, Hatfield, PA, USA) with a thin carbon film for 1 min and the excess solution was blotted with filter paper. Then, the grid was washed with a clean drop (~35 uL/drop) of water and stained two times with two drops (~25 uL/drop) of 2% (w/v) uranyl acetate (UA) for 10 s, 30 s respectively before air-drying.
GridModel: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
DetailsT4 DNA ligase and nicked double-stranded DNA substrate were mixed at a molar ratio of 1:1

-
Electron microscopy

MicroscopeTFS TALOS F200C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 3765 / Average exposure time: 1.0 sec. / Average electron dose: 160.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 9204
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3306
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
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