[English] 日本語
Yorodumi
- EMDB-5220: The architecture of the DNA polymerase-PCNA-DNA ternary complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5220
TitleThe architecture of the DNA polymerase-PCNA-DNA ternary complex
Map dataThis is a map of PolB-PCNA-DNA complex
SamplePyrococcus furiosus PolB-PCNA-DNA:
DNA polymerase / proliferating cell nuclear antigen / nucleic-acidNucleic acid
KeywordsDNA replication / DNA clamp
SourcePyrococcus furiosus (archaea) / unidentified (others)
Methodsingle particle reconstruction / 19 Å resolution
AuthorsMayanagi K / Nishida H / Kiyonari S / Saito M / Kohda D / Ishino Y / Shirai T / Morikawa K
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.
Authors: Kouta Mayanagi / Shinichi Kiyonari / Hirokazu Nishida / Mihoko Saito / Daisuke Kohda / Yoshizumi Ishino / Tsuyoshi Shirai / Kosuke Morikawa
DateDeposition: Jul 23, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Aug 22, 2012 / Last update: Aug 22, 2012

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_5220.map.gz (map file in CCP4 format, 687 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
56 pix
3.1 Å/pix.
= 173.6 Å
56 pix
3.1 Å/pix.
= 173.6 Å
56 pix
3.1 Å/pix.
= 173.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.1 Å
Density
Contour Level:2.25 (by author), 2.25 (movie #1):
Minimum - Maximum-3.8578527 - 8.5686512
Average (Standard dev.)-2E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions565656
Origin-9-9-9
Limit464646
Spacing565656
CellA=B=C: 173.59999 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-9-9-9
NC/NR/NS565656
D min/max/mean-3.8588.569-0.000

-
Supplemental data

-
Sample components

-
Entire Pyrococcus furiosus PolB-PCNA-DNA

EntireName: Pyrococcus furiosus PolB-PCNA-DNA / Details: The sample was monodisperse / Number of components: 3
Oligomeric State: One PolB binds to one trimer of PCNA and primed DNA
MassTheoretical: 210 kDa

-
Component #1: protein, DNA polymerase

ProteinName: DNA polymerase / a.k.a: PolB / Oligomeric Details: monomer / Recombinant expression: No
MassTheoretical: 104 kDa
SourceSpecies: Pyrococcus furiosus (archaea)

-
Component #2: protein, proliferating cell nuclear antigen

ProteinName: proliferating cell nuclear antigen / a.k.a: PCNAProliferating cell nuclear antigen / Oligomeric Details: trimer / Recombinant expression: Yes
MassTheoretical: 104 kDa
SourceSpecies: Pyrococcus furiosus (archaea)

-
Component #3: nucleic-acid, DNA

Nucleic-acidName: DNA / a.k.a: DNA / Class: DNA / Structure: DOUBLE HELIX / Synthetic: Yes
MassTheoretical: 23 kDa
SourceSpecies: unidentified (others)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.02 mg/ml / Buffer solution: 50 mM Tris-HCl,5 mM MgCl2 / pH: 8
Support film200 mesh Cu grid with carbon support film
VitrificationInstrument: NONE / Cryogen name: NONE

-
Electron microscopy imaging

ImagingMicroscope: JEOL 1010 / Details: minimum dose
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
LensMagnification: 400000 X (nominal)
Astigmatism: objective astigmatism was corrected using a quadrupole stigmator at 400,000 times magnification.
Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Side entry standard / Model: JEOL
CameraDetector: GENERIC GATAN

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 18897 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: common lines / Software: EMAN, IMAGIC / Resolution: 19 Å / Resolution method: FSC 0.5

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more