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The architecture of the DNA polymerase-PCNA-DNA ternary complex

by single particle reconstruction, at 19 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.25, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.25, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5220
TitleThe architecture of the DNA polymerase-PCNA-DNA ternary complex
MapThis is a map of PolB-PCNA-DNA complex
SamplePyrococcus furiosus PolB-PCNA-DNA
KeywordsDNA replication, DNA clamp
AuthorsMayanagi K, Nishida H, Kiyonari S, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa K
DateDeposition: 2010-07-23, Header release: 2010-12-08, Map release: 2012-08-22, Last update: 2012-08-22
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.25, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.25, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 5, Page 1845-1849, Year 2011
TitleArchitecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.
AuthorsKouta Mayanagi, Shinichi Kiyonari, Hirokazu Nishida, Mihoko Saito, Daisuke Kohda, Yoshizumi Ishino, Tsuyoshi Shirai, Kosuke Morikawa
Medical Institute of Bioregulation, Kyushu University and Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan.
KeywordsDNA (chemistry, 9007-49-2), DNA Polymerase beta (chemistry, 2.7.7.-), Glutamic Acid (metabolism), Microscopy, Electron, Models, Molecular, Proliferating Cell Nuclear Antigen (chemistry), Pyrococcus (enzymology), Streptavidin (metabolism, 9013-20-1)
LinksPubMed: 21245343, DOI: 10.1073/pnas.1010933108, PMC: PMC3033280
Map
Fileemd_5220.map.gz ( map file in CCP4 format, 687 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
56 pix
3.1 A/pix
= 173.6 A
56 pix
3.1 A/pix
= 173.6 A
56 pix
3.1 A/pix
= 173.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.25 (by author), 2.25 (movie #1):
Minimum - Maximum: -3.8578527 - 8.5686512
Average (Standard dev.): -2E-8 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions565656
Origin-9-9-9
Limit464646
Spacing565656
Unit CellA= B= C: 173.59999 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.1 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.13.13.1
M x/y/z565656
origin x/y/z0.0000.0000.000
length x/y/z173.600173.600173.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-9-9-9
NC/NR/NS565656
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.8588.569-0.000
Annotation DetailsThis is a map of PolB-PCNA-DNA complex
Supplement
Images
Images
Sample
NamePyrococcus furiosus PolB-PCNA-DNA
Number of Components3
Oligomeric StateOne PolB binds to one trimer of PCNA and primed DNA
Theoretical Mass0.21MDa
DetailsThe sample was monodisperse
Component #1: protein - PolB
Scientific nameDNA polymerase
Common NamePolB
Theoretical Mass0.104 MDa
Oligomeric Detailsmonomer
Scientific Name of SpeciesPyrococcus furiosus
NCBI taxonomy2261
Recombinant expressionNo
Component #2: protein - PCNA
Scientific nameproliferating cell nuclear antigen
Common NamePCNA
Theoretical Mass0.104 MDa
Oligomeric Detailstrimer
Scientific Name of SpeciesPyrococcus furiosus
NCBI taxonomy2261
Recombinant expressionYes
Component #3: nucleic-acid - DNA
Scientific nameDNA
Theoretical Mass0.023 MDa
Scientific Name of Speciesunidentified
NCBI taxonomy32644
ClassDNA
StructureDOUBLE HELIX
SyntheticYes
Experiment
Sample Preparation
Specimen Conc0.02 mg/ml
Specimen Support Details200 mesh Cu grid with carbon support film
Specimen Stateparticle
BufferDetails: 50 mM Tris-HCl,5 mM MgCl2
pH: 8
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 1010
Detailsminimum dose
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage100 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 400000
Astigmatismobjective astigmatism was corrected using a quadrupole stigmator at 400,000 times magnification.
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderSide entry standard
ModelJEOL
Camera
DetectorGENERIC GATAN
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmcommon lines
SoftwareEMAN, IMAGIC
Resolution By Author19 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections18897
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-5220.xml (7.4 KB)
Map dataemd_5220.map.gz (217.7 KB)
Imagesemd_5220_1.jpg (29.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5220
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 27.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 27.3 KB