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3D reconstruction of heterodimeric yeast Pol alpha using electron microscopy

by single particle reconstruction, at 22.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.045, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.045, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1618
Title3D reconstruction of heterodimeric yeast Pol alpha using electron microscopy
Map3D reconstruction of heterodimeric yeast Pol alpha using electron microscopy
SampleYeast DNA polymerase alpha
KeywordsDNA replication, DNA Polymerase alpha, Electron microscopy
AuthorsKlinge S, Nunez-Ramirez R, Llorca O, Pellegrini L
DateDeposition: 2009-05-04, Header release: 2009-05-07, Map release: 2011-05-06, Last update: 2011-05-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.045, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.045, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 28, Issue 13, Page 1978-87, Year 2009
Title3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases.
AuthorsSebastian Klinge, Rafael Núñez-Ramírez, Oscar Llorca, Luca Pellegrini
Department of Biochemistry, University of Cambridge, Cambridge, UK.
KeywordsAmino Acid Sequence, Animals, Crystallography, X-Ray, DNA Polymerase I (chemistry, 2.7.7.-), Escherichia coli (genetics), Humans, Microscopy, Electron, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Structure, Tertiary, Protein Subunits (chemistry), Saccharomyces cerevisiae (enzymology), Sequence Alignment
LinksDOI: 10.1038/emboj.2009.150, PubMed: 19494830, PMC: PMC2693882
Map
Fileemd_1618.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
3.8 A/pix
= 243.2 A
64 pix
3.8 A/pix
= 243.2 A
64 pix
3.8 A/pix
= 243.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum: -0.0982105 - 0.13849
Average (Standard dev.): 0.00211433 (0.0123166)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
Unit CellA= B= C: 243.2 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.8 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.83.83.8
M x/y/z646464
origin x/y/z-0.000-0.000-0.000
length x/y/z243.200243.200243.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0980.1380.002
Annotation Details3D reconstruction of heterodimeric yeast Pol alpha using electron microscopy
Supplement
Images
Images
Sample
NameYeast DNA polymerase alpha
Number of Components2
Oligomeric StateOne monomer of DNA polymerase alpha binds to a monomer of B-subunit
Theoretical Mass0.185MDa
Mass-estimation MethodGel Filtration
Component #1: protein - DNA polymerase alpha
Scientific nameDNA polymerase alpha
Theoretical Mass0.13 MDa
Experimental Mass0.13 MDa
Oligomeric DetailsDimer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
LinksGene Ontology: GO:0005658, GO:0005739, GO:0003677, GO:0003887, GO:0001882, GO:0000166, GO:0005515, GO:0006270, GO:0000731, GO:0006273, GO:0006279, GO:0006278, Inter Pro: IPR:006172, IPR:006134, IPR:017966, IPR:017964, IPR:006133, IPR:004578, IPR:015088
Component #2: protein - B subunit
Scientific nameB subunit
Theoretical Mass0.055 MDa
Experimental Mass0.055 MDa
Oligomeric DetailsDimer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
LinksInter Pro: IPR:007185, IPR:016722, IPR:013627, Gene Ontology: GO:0005658, GO:0005635, GO:0003677, GO:0003887, GO:0005515, GO:0006270, GO:0006273, GO:0016233
Experiment
Sample Preparation
StainingA diluted solution of Pol alpha complex was adsorbed onto glow-discharged carbon coated grids, stained with 2% uranyl formate
Specimen Conc0.7 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 100mM TrisHCl pH 8.0, 500 mM NaCl
pH: 8
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 1230
Date20-AUG-2009
DetailsMicroscope used JEOL-1230
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage100 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
AstigmatismObjective lens astigmatism was corrected at 120,000 times magnification
Nominal Cs2.9 mm
Imaging ModeBRIGHT FIELD
Defocus750 nm - 1200 nm
Specimen Holder
HolderEucentric
ModelJEOL
Temperature293 K ( 293 - 293 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerOTHER
Number of Digital Images170
Sampling Size10
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmML3D
SoftwareEMAN, Xmipp
CTF Correctionreverse phases
Resolution By Author22.9 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages190
Number of Projections12913
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body
Refinement Protocolrigid body
Refinement SpaceREAL
Target Criteriacross-correlation
Softwareadpem
PDB Entry ID3FLO
Model #1
Refinement SpaceREAL
Target Criteriacross-correlation
Refinement Protocolrigid body
DetailsProtocol: Rigid Body
Softwareadpem
PDB Entry ID2VWJ
Download
Data from EMDB
Header (meta data in XML format)emd-1618.xml (10.6 KB)
Map dataemd_1618.map.gz (68.5 KB)
ImagesEMD-1618.tif (1.6 MB)
emd_1618.tif (1.6 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1618
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.1 KB