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- EMDB-1148: Quaternary polymorphism of replicative helicase G40P: structural ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1148
TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Map dataBacteriophage SPP1 N-terminal deletion mutant helicase G40PN109: C6 architecture
Sample
  • Sample: N-terminal deletion mutant of G40P helicase of Bacteriophague SPP1
  • Protein or peptide: helicase
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsNunez-Ramirez R / Robledo Y / mesa P / Alonso JC
CitationJournal: J Mol Biol / Year: 2006
Title: Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Authors: Rafael Núñez-Ramírez / Yolanda Robledo / Pablo Mesa / Silvia Ayora / Juan Carlos Alonso / José María Carazo / Luis Enrique Donate /
Abstract: Quaternary polymorphism is a distinctive structural feature of the DnaB family of replicative DNA hexameric helicases. The Bacillus subtilis bacteriophage SPP1 gene 40 product (G40P) belongs to this ...Quaternary polymorphism is a distinctive structural feature of the DnaB family of replicative DNA hexameric helicases. The Bacillus subtilis bacteriophage SPP1 gene 40 product (G40P) belongs to this family. Three different quaternary states have been described for G40P homohexamers, two of them with C(3) symmetry, and the other with C(6) symmetry. We present three-dimensional reconstructions of the different architectures of G40P hexamers and a variant lacking the N-terminal domain. Comparison of the G40P and the deletion mutant structures sheds new light on the functional roles of the N and C-terminal domains, at the same time that it allows the direct structural mapping of these domains. Based on this new information, hybrid EM/X-ray models are presented for all the different symmetries. These results suggest that quaternary polymorphism of hexameric helicases may be implicated in the translocation along the DNA.
History
DepositionAug 5, 2005-
Header (metadata) releaseAug 5, 2005-
Map releaseMay 17, 2006-
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: 0.005954
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.005954
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1148.gif

Downloads & links

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Map

FileDownload / File: emd_1148.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage SPP1 N-terminal deletion mutant helicase G40PN109: C6 architecture
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 64 pix.
= 262.4 Å		4.1 Å/pix.
x 64 pix.
= 262.4 Å		4.1 Å/pix.
x 64 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00239 / Movie #1: 0.005954
Minimum - Maximum-0.0205899 - 0.0228645
Average (Standard dev.)0.0000337599 (±0.00230229)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 262.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0210.0230.000

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Supplemental data

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Sample components

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Entire : N-terminal deletion mutant of G40P helicase of Bacteriophague SPP1

EntireName: N-terminal deletion mutant of G40P helicase of Bacteriophague SPP1
Components
  • Sample: N-terminal deletion mutant of G40P helicase of Bacteriophague SPP1
  • Protein or peptide: helicase

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Supramolecule #1000: N-terminal deletion mutant of G40P helicase of Bacteriophague SPP1

SupramoleculeName: N-terminal deletion mutant of G40P helicase of Bacteriophague SPP1
type: sample / ID: 1000 / Oligomeric state: Homohexamer / Number unique components: 1
Molecular weightExperimental: 240 KDa / Theoretical: 240 KDa / Method: gel filtration chromatography

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Macromolecule #1: helicase

MacromoleculeName: helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Bacillus phage SPP1 (virus) / Strain: SPP1 / Cell: Bacteria
Molecular weightExperimental: 240 KDa / Theoretical: 240 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pCB506

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.17 mg/mL
BufferpH: 7
Details: 50mM HEPES, 50mM NaCl, 10mM MgCl2, 1mM ATP, 1mM dithithreitol
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

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Electron microscopy

MicroscopeJEOL 2000EX
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 54 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Xmipp / Number images used: 8000

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