[English] 日本語
Yorodumi
- EMDB-1225: Loading a ring: structure of the Bacillus subtilis DnaB protein, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1225
TitleLoading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase.
Map dataBacillus subtilis DnaB
Sample
  • Sample: Bacillus subtilis DnaB
  • Protein or peptide: DnaB
Function / homology:
Function and homology information
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsNunez-Ramirez R / Velten M / Rivas G / Polard P / Carazo JM / Donate LE
CitationJournal: J Mol Biol / Year: 2007
Title: Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase.
Authors: Rafael Núñez-Ramírez / Marion Velten / Germán Rivas / Patrice Polard / José María Carazo / Luis Enrique Donate /
Abstract: Loading of the ring-shaped replicative helicase is a critical step in the initiation of DNA replication. Bacillus subtilis has adopted a two-protein strategy to load its hexameric replicative ...Loading of the ring-shaped replicative helicase is a critical step in the initiation of DNA replication. Bacillus subtilis has adopted a two-protein strategy to load its hexameric replicative helicase: DnaB and DnaI interact with the helicase and mediate its delivery onto DNA. We present here the 3D electron microscopy structure of the DnaB protein, along with a detailed analysis of both its oligomeric state and its domain organization. DnaB is organized as an asymmetric tetramer that is comprised of two stacked components, one arranged as a closed collar and the other as an open sigma shape. Intriguingly, the 3D map of DnaB exhibits an overall architecture similar to the structure of the Escherichia coli gamma-complex, the loader of the ring-shaped processivity factor. We propose a model whereby each DnaB monomer participates in both stacked components of the tetramer and displays a different overall shape. This asymmetric quaternary organization could be a general feature of ring loaders.
History
DepositionApr 25, 2006-
Header (metadata) releaseMay 16, 2006-
Map releaseMay 16, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.304519715
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.304519715
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1225.gif

Downloads & links

-
Map

FileDownload / File: emd_1225.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacillus subtilis DnaB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 64 pix.
= 256. Å		4 Å/pix.
x 64 pix.
= 256. Å		4 Å/pix.
x 64 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.24 / Movie #1: 4.3045197
Minimum - Maximum-4.78986 - 8.93615
Average (Standard dev.)-0.0355513 (±0.939863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin111
Dimensions646464
Spacing646464
CellA=B=C: 256 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS646464
D min/max/mean-4.7908.936-0.036

-
Supplemental data

-
Sample components

-
Entire : Bacillus subtilis DnaB

EntireName: Bacillus subtilis DnaB
Components
  • Sample: Bacillus subtilis DnaB
  • Protein or peptide: DnaB

-
Supramolecule #1000: Bacillus subtilis DnaB

SupramoleculeName: Bacillus subtilis DnaB / type: sample / ID: 1000 / Oligomeric state: Homotetramer / Number unique components: 1
Molecular weightExperimental: 200 KDa / Theoretical: 200 KDa
Method: Sedimentation equilibrium by analytical ultracentrifugation

-
Macromolecule #1: DnaB

MacromoleculeName: DnaB / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Bacillus subtilis (bacteria) / Cell: Bacteria / Location in cell: Plasma membrane
Molecular weightExperimental: 200 KDa / Theoretical: 200 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pSMG37
SequenceInterPro: INTERPRO: IPR010833

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.088 mg/mL
BufferpH: 7.5 / Details: 50mM Tris-HCl, 50mM NaCl, 2mM MgCl2 and 1mM DTT
StainingType: NEGATIVE
Details: Grids with adsorbed protein stained on 2% uranyl acetate for 1 minute
GridDetails: collodion/carbon coated 400 mesh copper grid
VitrificationCryogen name: NONE

-
Electron microscopy

MicroscopeJEOL 2000EX
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 20 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp and EMAN / Number images used: 8352

+
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