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Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.

by single particle reconstruction, at 24 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0493, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0493, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1147
TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
MapBacteriophage SPP1 helicase G40P: C3 architecture
SampleC3 architecture of Bacteriophage SPP1
AuthorsNunez-Ramirez R, Robledo Y, mesa P, Alonso JC
DateDeposition: 2005-08-05, Header release: 2005-08-05, Map release: 2006-05-17, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0493, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0493, Made by UCSF CHIMERA

Supplemental images

1147.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1135
Cite

EMDB-1146
Cite

EMDB-1148
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1146

EMDB-1135

EMDB-1148
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 357, Issue 4, Page 1063-76, Year 2006
TitleQuaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
AuthorsRafael Núñez-Ramírez, Yolanda Robledo, Pablo Mesa, Silvia Ayora, Juan Carlos Alonso, José María Carazo, Luis Enrique Donate
Department of Macro-molecular Structure, Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
KeywordsAmino Acid Sequence, DNA Helicases (chemistry, 3.6.1.-), G40P helicase protein, Bacteriophage SPP1 (5.99.-), Models, Molecular, Molecular Sequence Data, Protein Isoforms (chemistry), Protein Structure, Quaternary, Sequence Alignment, Viral Proteins (chemistry)
LinksPII: S0022-2836(06)00144-6, DOI: 10.1016/j.jmb.2006.01.091, PubMed: 16490212
Map
FileEMD-1147.map ( map file in CCP4 format, 2049 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.0243, 0.0493 (movie #1):
Minimum - Maximum: -0.157662 - 0.18685
Average (Standard dev.): 0.000114719 (0.0121095)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 80 80 80
Origin : 0 0 0
Limit : 79 79 79
Spacing : 80 80 80
Unit CellA = 328 A , B = 328 A , C = 328 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 4.1 A , Y = 4.1 A , Z = 4.1 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.1580.1870.000
Annotation DetailsBacteriophage SPP1 helicase G40P: C3 architecture
Supplement
Images
Images

1147.gif
Sample
NameC3 architecture of Bacteriophage SPP1
Oligomeric StateHomohexamer
Number of Components1
Experimental Mass0.3 MDa
Theoretical Mass0.3 MDa
Mass-estimation Methodgel filtration chromatography
Component #1: protein - helicase
Scientific namehelicase
Theoretical Mass0.3 MDa
Experimental Mass0.3 MDa
Oligomeric DetailsHexamer
Number of Copies6
Scientific Name of SpeciesBacillus phage SPP1 (NCBI Taxonomy: 10724)
StrainSPP1
Recombinant expressionYes
Natural SourceCell: Bacteria
Engineered SourceVector: pCB506
Exp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc0.2 mg/ml
StainingGrids with adsorbed protein stained on 2% uranyl acetate for 1 minute
Specimen Support Detailscollodion/carbon coated 400 mesh copper grid
Specimen Stateparticle
BufferDetails: 50mM HEPES, 50mM NaCl, 10mM MgCl2, 1mM ATP, 1mM dithithreitol
pH: 7.0
Vitrification
Cryogen NameNONE
Imaging
MicroscopeJEOL 2000EX
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage80 kV
Electron Dose20 e/A**2
Illumination ModeOTHER
Lens
MagnificationNominal: 60000 X,
Imaging ModeOTHER
Specimen Holder
HolderEucentric ( OTHER )
Camera
DetectorKodak SO163
Image Acquisition
Number of Digital Images40
Sampling Size21 microns
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmRandom Conical Tilt
SoftwareSPIDER Xmipp
Resolution By Author24
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections700
Download
Data from EMDB
Header (meta data in XML format)emd-1147.xml (6.7 KB)
Map dataemd_1147.map.gz (1.8 MB)
Images1147.gif (7.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1147
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.2 MB
Session file for UCSF-Chimera, 26.6 KB