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

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Basic information

Entry
Database: EMDB / ID: 1135
TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Map dataBacteriophage SPP1 helicase G40P: C6 architecture
SampleC6 architecture of Bacteriophage SPP1 replicative helicase G40P:
helicase
SourceBacillus phage SPP1 (bacteriophage)
Methodsingle particle reconstruction / negative staining / 24 Å resolution
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.
DateDeposition: Jul 13, 2005 / Header (metadata) release: Jul 14, 2005 / Map release: May 16, 2006 / Last update: Oct 24, 2012

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Structure visualization

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

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Map

Fileemd_1135.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
4.1 Å/pix.
= 328. Å
80 pix
4.1 Å/pix.
= 328. Å
80 pix
4.1 Å/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
Contour Level:0.00292, 0.0053 (movie #1):
Minimum - Maximum-0.0147015 - 0.0285048
Average (Standard dev.)0.000101116 (0.0014075)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
CellA=B=C: 328 Å
α=β=γ: 90 deg.

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
Oligomeric State: Homohexamer / Number of components: 1
MassTheoretical: 300 kDa / Experimental: 300 kDa / Measured by: gel filtration chromatography

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Component #1: protein, helicase

ProteinName: helicase / Oligomeric Details: Hexamer / Recombinant expression: Yes / Number of Copies: 6
MassTheoretical: 300 kDa / Experimental: 300 kDa
SourceSpecies: Bacillus phage SPP1 (bacteriophage) / Strain: SPP1
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pCB506
Source (natural)Cell: Bacteria

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.2 mg/ml
Buffer solution: 50mM HEPES, 50mM NaCl, 10mM MgCl2, 1mM ATP, 1mM dithithreitol
pH: 7
Support filmcollodion/carbon coated 400 mesh copper grid
StainingGrids with adsorbed protein satined on 2% uranyl acetate for 1 minute
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2000EX
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Electron dose: 20 e/Å2 / Illumination mode: OTHER
LensMagnification: 60000 X (nominal) / Imaging mode: OTHER
Specimen HolderHolder: Eucentric / Model: OTHER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 40 / Scanner: ZEISS SCAI / Sampling size: 21 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 700 / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: Random Conical / Software: SPIDER Xmipp / Resolution: 24 Å / Resolution method: FSC 0.5

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