[English] 日本語
Yorodumi
- EMDB-0244: Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0244
TitleCryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Map datacryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
SampleComplex between DNA polymerase D and DNA duplex:
DNA polymerase D / DNA / (DNA polymerase II ...) x 2 / (nucleic-acidNucleic acid) x 2 / (ligand) x 2
Function / homologyIntein N-terminal splicing region / DNA polymerase II large subunit DP2 / Hint domain superfamily / Intein C-terminal splicing region / DNA polymerase delta/II small subunit family / DNA polymerase II large subunit DP2, N-terminal / Nucleic acid-binding, OB-fold / DNA polymerase II small subunit, archaeal / Calcineurin-like phosphoesterase domain, ApaH type / DNA polymerase II large subunit DP2 ...Intein N-terminal splicing region / DNA polymerase II large subunit DP2 / Hint domain superfamily / Intein C-terminal splicing region / DNA polymerase delta/II small subunit family / DNA polymerase II large subunit DP2, N-terminal / Nucleic acid-binding, OB-fold / DNA polymerase II small subunit, archaeal / Calcineurin-like phosphoesterase domain, ApaH type / DNA polymerase II large subunit DP2 / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Intein C-terminal splicing motif profile. / Calcineurin-like phosphoesterase / exodeoxyribonuclease I / exodeoxyribonuclease I activity / DNA catabolic process, exonucleolytic / intein-mediated protein splicing / 3'-5' exonuclease activity / DNA-dependent DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / DNA polymerase II small subunit / DNA polymerase II large subunit
Function and homology information
SourcePyrococcus abyssi (archaea)
Methodsingle particle reconstruction / cryo EM / 7.1 Å resolution
AuthorsRaia P / Carroni M / Sauguet L
CitationJournal: PLoS Biol. / Year: 2019
Title: Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.
Authors: Pierre Raia / Marta Carroni / Etienne Henry / Gérard Pehau-Arnaudet / Sébastien Brûlé / Pierre Béguin / Ghislaine Henneke / Erik Lindahl / Marc Delarue / Ludovic Sauguet
Validation ReportPDB-ID: 6hms

SummaryFull reportAbout validation report
DateDeposition: Sep 12, 2018 / Header (metadata) release: Oct 10, 2018 / Map release: Jan 30, 2019 / Last update: Jan 30, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hms
  • Surface level: 0.58
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0244.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.36 Å/pix.
= 299.2 Å
220 pix
1.36 Å/pix.
= 299.2 Å
220 pix
1.36 Å/pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour Level:0.58 (by author), 0.58 (movie #1):
Minimum - Maximum-3.568817 - 3.8639772
Average (Standard dev.)0.0047397213 (0.42160863)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin0.00.00.0
Limit219.0219.0219.0
Spacing220220220
CellA=B=C: 299.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z299.200299.200299.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.6581.6240.005

-
Supplemental data

-
Sample components

+
Entire Complex between DNA polymerase D and DNA duplex

EntireName: Complex between DNA polymerase D and DNA duplex / Number of components: 9

+
Component #1: protein, Complex between DNA polymerase D and DNA duplex

ProteinName: Complex between DNA polymerase D and DNA duplex / Recombinant expression: No

+
Component #2: protein, DNA polymerase D

ProteinName: DNA polymerase D / Recombinant expression: No
SourceSpecies: Pyrococcus abyssi (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: Pyrococcus abyssi (archaea)
Source (engineered)Expression System: synthetic construct (others)

+
Component #4: protein, DNA polymerase II small subunit

ProteinName: DNA polymerase II small subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.078012 kDa
SourceSpecies: Pyrococcus abyssi (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, DNA polymerase II large subunit,DNA polymerase II large ...

ProteinName: DNA polymerase II large subunit,DNA polymerase II large subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 144.418969 kDa
SourceSpecies: Pyrococcus abyssi (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #6: nucleic-acid, DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*T...

Nucleic-acidName: DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DA)(DG)(DA)(DC)(DG)(DG)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DC)
MassTheoretical: 4.635998 kDa
SourceSpecies: Pyrococcus abyssi (archaea)

+
Component #7: nucleic-acid, DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*...

Nucleic-acidName: DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC) (DC)(DG)(DT)(DC)(DT)(DC)
MassTheoretical: 4.851129 kDa
SourceSpecies: Pyrococcus abyssi (archaea)

+
Component #8: ligand, FE (III) ION

LigandName: FE (III) ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.584505 MDa

+
Component #9: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 8774
3D reconstructionSoftware: cryoSPARC / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
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

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