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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
AuthorsKlinge S, Nunez-Ramirez R, Llorca O, Pellegrini L
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

EMD-1618.tif

emd_1618.tif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3flo
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1104

EMDB-1103

PDB-1zo1
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 ( map file in CCP4 format, 1050 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:0.045 (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 Order : X Y Z
Dimensions : 64 64 64
Origin : 0 0 0
Limit : 63 63 63
Spacing : 64 64 64
Unit CellA = 243.2 A , B = 243.2 A , C = 243.2 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 3.8 A , Y = 3.8 A , 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

EMD-1618.tif

emd_1618.tif
Sample
NameYeast DNA polymerase alpha
Number of Components2
Oligomeric StateOne monomer of DNA polymerase alpha binds to a monomer of B-subunit
Theoretical Mass0.185 MDa
Mass-estimation MethodGel Filtration
Component #1: protein - DNA polymerase alpha
Scientific nameDNA polymerase alpha
Theoretical Mass0.130 MDa
Experimental Mass0.130 MDa
Oligomeric DetailsDimer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesBaker's yeast
Recombinant expressionYes
LinksGene Ontology: GO:0005658, Gene Ontology: GO:0005739, Gene Ontology: GO:0003677, Gene Ontology: GO:0003887, Gene Ontology: GO:0001882, Gene Ontology: GO:0000166, Gene Ontology: GO:0005515, Gene Ontology: GO:0006270, Gene Ontology: GO:0000731, Gene Ontology: GO:0006273, Gene Ontology: GO:0006279, Gene Ontology: GO:0006278, InterPro: IPR:006172, InterPro: IPR:006134, InterPro: IPR:017966, InterPro: IPR:017964, InterPro: IPR:006133, InterPro: IPR:004578, InterPro: 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 (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's yeast
Recombinant expressionYes
LinksInterPro: IPR:007185, InterPro: IPR:016722, InterPro: IPR:013627, Gene Ontology: GO:0005658, Gene Ontology: GO:0005635, Gene Ontology: GO:0003677, Gene Ontology: GO:0003887, Gene Ontology: GO:0005515, Gene Ontology: GO:0006270, Gene Ontology: GO:0006273, Gene Ontology: 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: 8.0
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeOTHER
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 X,
AstigmatismObjective lens astigmatism was corrected at 120,000 times magnification
Nominal Cs2.9 mm
Imaging ModeBRIGHT FIELD
Defocus750 nm - 1200 nm
Specimen Holder
HolderEucentric ( JEOL )
Temperature293 Kelvin ( 293 Kelvin - 293 Kelvin )
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerOTHER
Number of Digital Images170
Sampling Size10 microns
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmML3D
SoftwareEMAN, Xmipp
CTF Correctionreverse phases
Resolution By Author22.9
Resolution MethodFSC at 0.5 cut-off
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
Model #1
Refinement SpaceREAL
Target Criteriacross-correlation
Refinement Protocolrigid body
DetailsProtocol: Rigid Body
Softwareadpem
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