[English] 日本語
Yorodumi
- EMDB-50145: Pyrococcus abyssi PolD-Rpa2 winged helix domain complex class 2 D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50145
TitlePyrococcus abyssi PolD-Rpa2 winged helix domain complex class 2 DP1 subunit local refinement
Map data
Sample
  • Complex: PolD-Rpa2 winged-helix domain complex from Pyrococcus abyssi
    • Protein or peptide: PolD DP1 subunit
KeywordsDNA Polymerase / Archaea / replication / RPA
Biological speciesPyrococcus abyssi GE5 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMartinez-Carranza M / Sauguet L
Funding support France, European Union, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: Nat Commun / Year: 2024
Title: Communication between DNA polymerases and Replication Protein A within the archaeal replisome.
Authors: Markel Martínez-Carranza / Léa Vialle / Clément Madru / Florence Cordier / Ayten Dizkirici Tekpinar / Ahmed Haouz / Pierre Legrand / Rémy A Le Meur / Patrick England / Rémi Dulermo / J ...Authors: Markel Martínez-Carranza / Léa Vialle / Clément Madru / Florence Cordier / Ayten Dizkirici Tekpinar / Ahmed Haouz / Pierre Legrand / Rémy A Le Meur / Patrick England / Rémi Dulermo / J Iñaki Guijarro / Ghislaine Henneke / Ludovic Sauguet /
Abstract: Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. ...Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site. Finally, RPA is shown to stimulate the activity of PriSL in a WH-dependent manner. This study provides a molecular understanding of the WH-mediated regulatory activity in central replication factors such as RPA, which regulate genome maintenance in Archaea and Eukaryotes.
History
DepositionApr 22, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50145.png

Downloads & links

-
Map

FileDownload / File: emd_50145.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 350 pix.
= 336. Å		0.96 Å/pix.
x 350 pix.
= 336. Å		0.96 Å/pix.
x 350 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.8153636 - 3.8664293
Average (Standard dev.)0.0004601322 (±0.058022365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50145_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_50145_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_50145_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PolD-Rpa2 winged-helix domain complex from Pyrococcus abyssi

EntireName: PolD-Rpa2 winged-helix domain complex from Pyrococcus abyssi
Components
  • Complex: PolD-Rpa2 winged-helix domain complex from Pyrococcus abyssi
    • Protein or peptide: PolD DP1 subunit

-
Supramolecule #1: PolD-Rpa2 winged-helix domain complex from Pyrococcus abyssi

SupramoleculeName: PolD-Rpa2 winged-helix domain complex from Pyrococcus abyssi
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 230 KDa

-
Macromolecule #1: PolD DP1 subunit

MacromoleculeName: PolD DP1 subunit / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGKHHHHSGH HHTGHHHHSG SHHHTSSSAS TGENLYFQGT GDGSDELVKA LERAGYLLTP SAYYLLVDHF KEGKFSLVEL VKFAKSKGVF IIDGDLAYEF LQFLGLGVPQ EIKESYISTG EEAEKTVESQ ETRASELEEG GVSQVSSGEL QELKEESPEI STTEEEIGGL ...String:
MGKHHHHSGH HHTGHHHHSG SHHHTSSSAS TGENLYFQGT GDGSDELVKA LERAGYLLTP SAYYLLVDHF KEGKFSLVEL VKFAKSKGVF IIDGDLAYEF LQFLGLGVPQ EIKESYISTG EEAEKTVESQ ETRASELEEG GVSQVSSGEL QELKEESPEI STTEEEIGGL ELVQSSISTG SEVEYNNGEN GESVVVLDKY GYPILYAPEE IGEEKEYSKY EDVVIEWNPS VTPVQIEKNY EVKFDVRQVK LRPPKVKNGS GKEGEIIVEA YASLFKSRLS KLKRILRENP EISNVVDIGK LNYVSGDEEV TIIGLVNSKR ETNRGLIFEV EDKTGIVKVF LPKDSEDYRE AFKVLPDAVV AFKGFYSKKG IFFANKFYLP DVPLYRKQKP PLEEKVYAIL ISDIHVGSRE FCEKAFLKFL EWLNGHVESK EEEEIVSRVK YLIIAGDVVD GIGIYPGQYS DLVIPDIFDQ YEALANLLAN VPEHITMFIG PGNADAARPA IPQPEFYKEY AKPIYKLKNA IIISNPAVIR LHGRDFLIAH GRGIEDVVSF VPGLTHHKPG LPMVELLKMR HLAPTFGGKV PIAPDPEDLL VIEEVPDLVQ MGHVHVYDAV VYRGVQLVNS ATWQAQTEFQ KMVNIVPTPA KVPVVDVESA RVVKVLDFSG WC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6t8h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 174709
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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