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- EMDB-1017: The DnaB.DnaC complex: a structure based on dimers assembled arou... -

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Basic information

Entry
Database: EMDB / ID: EMD-1017
TitleThe DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.
Map data
Sample
  • Sample: DnaB.DnaC complex from Escherichia coli
  • Protein or peptide: DnaB
  • Protein or peptide: DnaC
Function / homology: / DNA helicase activity
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsBarcena M / Ruiz T / Donate LE / Brown SE / Dixon NE / Radermacher M / Carazo JM
CitationJournal: EMBO J / Year: 2001
Title: The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.
Authors: M Bárcena / T Ruiz / L E Donate / S E Brown / N E Dixon / M Radermacher / J M Carazo /
Abstract: Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three- ...Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face.
History
DepositionJun 26, 2002-
Header (metadata) releaseOct 17, 2002-
Map releaseOct 17, 2003-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1017.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.6 Å
Density
Contour Level1: 0.00411 / Movie #1: 0.012
Minimum - Maximum-0.0212883 - 0.0298335
Average (Standard dev.)0.0000559347 (±0.0016241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 460.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.63.63.6
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0210.0300.000

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Supplemental data

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Sample components

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Entire : DnaB.DnaC complex from Escherichia coli

EntireName: DnaB.DnaC complex from Escherichia coli
Components
  • Sample: DnaB.DnaC complex from Escherichia coli
  • Protein or peptide: DnaB
  • Protein or peptide: DnaC

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Supramolecule #1000: DnaB.DnaC complex from Escherichia coli

SupramoleculeName: DnaB.DnaC complex from Escherichia coli / type: sample / ID: 1000
Oligomeric state: one homohexamer of DnaB binds to six monomers of DnaC
Number unique components: 2
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: DnaB

MacromoleculeName: DnaB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: cytoplasma
Molecular weightTheoretical: 310 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: An1459/pPA569
SequenceGO: DNA helicase activity / InterPro: INTERPRO: IPR001198

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Macromolecule #2: DnaC

MacromoleculeName: DnaC / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Oligomeric state: three dimers / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: cytoplasma
Molecular weightTheoretical: 170 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: An1459/pPA569

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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

Concentration0.03 mg/mL
BufferpH: 7.6
Details: 50 mM Tris-HCl, 25 mM NaCl 5 mM MgCl2 2 mM DTT 0.1 mM ATP
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: double-blotting

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 57874 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder: cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 35
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 58 / Bits/pixel: 8
Tilt angle min0

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: SPIDER and Xmipp / Number images used: 7888

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