[English] 日本語
Yorodumi
- EMDB-0723: PolD-PCNA-DNA (form A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0723
TitlePolD-PCNA-DNA (form A)
Map data
Sample
  • Complex: Thermococcus kodakarensis PolD-PCNA-DNA
    • Complex: Thermococcus kodakarensis Pol D DP1 subunit
    • Complex: Thermococcus kodakarensis Pol D DP2 subunit
    • Complex: Thermococcus kodakarensis PCNA trimer ring
    • Complex: pri25DNA
    • Complex: temp35DNA
KeywordsFamily D Polymerase / PCNA / Switch Hook / REPLICATION
Function / homology
Function and homology information


exodeoxyribonuclease I / DNA polymerase complex / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / intron homing / DNA catabolic process / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication ...exodeoxyribonuclease I / DNA polymerase complex / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / intron homing / DNA catabolic process / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA-templated DNA replication / endonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / identical protein binding
Similarity search - Function
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II small subunit, archaeal / : / DNA polymerase II small subunit, N-terminal domain / DNA polymerase delta/II small subunit family / LAGLIDADG-like domain / Intein splicing domain / Intein ...DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II small subunit, archaeal / : / DNA polymerase II small subunit, N-terminal domain / DNA polymerase delta/II small subunit family / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA polymerase II large subunit / DNA polymerase II small subunit / DNA polymerase sliding clamp 1
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsMayanagi K / Oki K / Miyazaki N / Ishino S / Yamagami T / Iwasaki K / Kohda D / Morikawa K / Shirai T / Ishino Y
Funding support Japan, 7 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K06089 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H01818 Japan
Japan Agency for Medical Research and Development (AMED)19am0101069j0003 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K05442 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26242075 Japan
Japan Science and TechnologyJPMJPR12L9 Japan
Japan Agency for Medical Research and Development (AMED)JP19am01010720231 Japan
CitationJournal: BMC Biol / Year: 2020
Title: Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Authors: Kouta Mayanagi / Keisuke Oki / Naoyuki Miyazaki / Sonoko Ishino / Takeshi Yamagami / Kosuke Morikawa / Kenji Iwasaki / Daisuke Kohda / Tsuyoshi Shirai / Yoshizumi Ishino /
Abstract: BACKGROUND: DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA ...BACKGROUND: DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3'-5' editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually required for the full activities of each enzyme. However, the processivity of the replicase holoenzyme has additionally been shown to be enhanced by the clamp molecule proliferating cell nuclear antigen (PCNA), making it crucial to elucidate the interaction between PolD and PCNA on a structural level for a full understanding of its functional relevance. We present here the 3D structure of a PolD-PCNA-DNA complex from Thermococcus kodakarensis using single-particle cryo-electron microscopy (EM).
RESULTS: Two distinct forms of the PolD-PCNA-DNA complex were identified by 3D classification analysis. Fitting the reported crystal structures of truncated forms of DP1 and DP2 from Pyrococcus ...RESULTS: Two distinct forms of the PolD-PCNA-DNA complex were identified by 3D classification analysis. Fitting the reported crystal structures of truncated forms of DP1 and DP2 from Pyrococcus abyssi onto our EM map showed the 3D atomic structural model of PolD-PCNA-DNA. In addition to the canonical interaction between PCNA and PolD via PIP (PCNA-interacting protein)-box motif, we found a new contact point consisting of a glutamate residue at position 171 in a β-hairpin of PCNA, which mediates interactions with DP1 and DP2. The DNA synthesis activity of a mutant PolD with disruption of the E171-mediated PCNA interaction was not stimulated by PCNA in vitro.
CONCLUSIONS: Based on our analyses, we propose that glutamate residues at position 171 in each subunit of the PCNA homotrimer ring can function as hooks to lock PolD conformation on PCNA for ...CONCLUSIONS: Based on our analyses, we propose that glutamate residues at position 171 in each subunit of the PCNA homotrimer ring can function as hooks to lock PolD conformation on PCNA for conversion of its activity. This hook function of the clamp molecule may be conserved in the three domains of life.
History
DepositionJul 31, 2019-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6knb
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0723.png

Downloads & links

-
Map

FileDownload / File: emd_0723.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 160 pix.
= 179.2 Å		1.12 Å/pix.
x 160 pix.
= 179.2 Å		1.12 Å/pix.
x 160 pix.
= 179.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0069 / Movie #1: 0.013
Minimum - Maximum-0.04713693 - 0.0777891
Average (Standard dev.)-0.00015306521 (±0.005071163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 179.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0470.078-0.000

-
Supplemental data

-
Sample components

-
Entire : Thermococcus kodakarensis PolD-PCNA-DNA

EntireName: Thermococcus kodakarensis PolD-PCNA-DNA
Components
  • Complex: Thermococcus kodakarensis PolD-PCNA-DNA
    • Complex: Thermococcus kodakarensis Pol D DP1 subunit
    • Complex: Thermococcus kodakarensis Pol D DP2 subunit
    • Complex: Thermococcus kodakarensis PCNA trimer ring
    • Complex: pri25DNA
    • Complex: temp35DNA

-
Supramolecule #1: Thermococcus kodakarensis PolD-PCNA-DNA

SupramoleculeName: Thermococcus kodakarensis PolD-PCNA-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#6

-
Supramolecule #2: Thermococcus kodakarensis Pol D DP1 subunit

SupramoleculeName: Thermococcus kodakarensis Pol D DP1 subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Thermococcus kodakarensis (archaea)

-
Supramolecule #3: Thermococcus kodakarensis Pol D DP2 subunit

SupramoleculeName: Thermococcus kodakarensis Pol D DP2 subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Thermococcus kodakarensis (archaea)

-
Supramolecule #4: Thermococcus kodakarensis PCNA trimer ring

SupramoleculeName: Thermococcus kodakarensis PCNA trimer ring / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Thermococcus kodakarensis (archaea)

-
Supramolecule #5: pri25DNA

SupramoleculeName: pri25DNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5
Details: Sequence:(DC)(DG)(DA)(DA)(DC)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DA)(DT)(DC)(DC)(DT)(DG)(DA)(DC)(DG)(DA)(DC)(DA)
Source (natural)Organism: synthetic construct (others)

-
Supramolecule #6: temp35DNA

SupramoleculeName: temp35DNA / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #6
Details: Sequence: (DG)(DT)(DT)(DC)(DG)(DC)(DT)(DA)(DC)(DA)(DT)(DG)(DT)(DC)(DG)(DT)(DC)(DA)(DG)(DG)(DA)(DT)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DG)(DT)(DT)(DC)(DG)
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41073
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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