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- EMDB-1135: Quaternary polymorphism of replicative helicase G40P: structural ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1135
TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Map dataBacteriophage SPP1 helicase G40P: C6 architecture
Sample
  • Sample: C6 architecture of Bacteriophage SPP1 replicative helicase G40P
  • Protein or peptide: helicase
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsNunez-Ramirez R / Robledo Y / mesa P / Alonso JC / Carazo JM / Donate LE
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
DepositionJul 13, 2005-
Header (metadata) releaseJul 14, 2005-
Map releaseMay 16, 2006-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0053
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0053
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1135.gif

Downloads & links

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Map

FileDownload / File: emd_1135.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage SPP1 helicase G40P: C6 architecture
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. 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: 0.00292 / Movie #1: 0.0053
Minimum - Maximum-0.0147015 - 0.0285048
Average (Standard dev.)0.000101116 (±0.0014075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
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/NS808080
D min/max/mean-0.0150.0290.000

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Supplemental data

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Sample components

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Entire : C6 architecture of Bacteriophage SPP1 replicative helicase G40P

EntireName: C6 architecture of Bacteriophage SPP1 replicative helicase G40P
Components
  • Sample: C6 architecture of Bacteriophage SPP1 replicative helicase G40P
  • Protein or peptide: helicase

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Supramolecule #1000: C6 architecture of Bacteriophage SPP1 replicative helicase G40P

SupramoleculeName: C6 architecture of Bacteriophage SPP1 replicative helicase G40P
type: sample / ID: 1000 / Oligomeric state: Homohexamer / Number unique components: 1
Molecular weightExperimental: 300 KDa / Theoretical: 300 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 / synonym: Bacteriphage SPP1 / Cell: Bacteria
Molecular weightExperimental: 300 KDa / Theoretical: 300 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

Concentration0.2 mg/mL
BufferpH: 7
Details: 50mM HEPES, 50mM NaCl, 10mM MgCl2, 1mM ATP, 1mM dithithreitol
StainingType: NEGATIVE
Details: Grids with adsorbed protein satined 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: 40 / 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: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER Xmipp / Number images used: 700

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