[English] 日本語
Yorodumi
- EMDB-76387: EcPriA bound to DNA replication fork with dsDNA lagging strand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76387
TitleEcPriA bound to DNA replication fork with dsDNA lagging strand
Map data
Sample
  • Complex: EcPriA bound to DNA replication fork with dsDNA lagging strand
    • Protein or peptide: E. coli PriA
    • DNA: Replication fork - Leading strand template
    • DNA: Replication fork - Lagging strand template
    • DNA: Replication fork - Leading nascent strand
    • DNA: Replication fork - Lagging nascent strand
KeywordsReplication Fork / Helicase / DNA BINDING PROTEIN
Function / homology
Function and homology information


DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / DNA 3'-5' helicase / DNA replication initiation / 3'-5' DNA helicase activity / response to gamma radiation / helicase activity ...DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / DNA 3'-5' helicase / DNA replication initiation / 3'-5' DNA helicase activity / response to gamma radiation / helicase activity / replication fork processing / DNA-templated DNA replication / double-strand break repair / DNA recombination / DNA replication / response to antibiotic / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / : / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / Primosomal protein N'-like, winged helix ...Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / : / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / Primosomal protein N'-like, winged helix / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replication restart protein PriA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDuckworth AT / Deorio HR / Grant T / Keck JL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098885 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Domain dynamics within the PriA DNA helicase regulate DNA replication restart.
Authors: Haley R Deorio / Alexander T Duckworth / Gavin R Forsythe / Andrew Y Sung / Steve J Sandler / Timothy Grant / James L Keck /
Abstract: Prematurely terminated DNA replication processes in bacteria must be restarted for successful genome duplication. In Escherichia coli, the PriA DNA helicase orchestrates replication restart by ...Prematurely terminated DNA replication processes in bacteria must be restarted for successful genome duplication. In Escherichia coli, the PriA DNA helicase orchestrates replication restart by assembling the PriA/PriB/DnaT preprimosome complex onto abandoned DNA replication forks and reloading the replicative machinery. We show that the structure of the replication fork lagging strand-whether single- or double-stranded-influences the position of the cysteine-rich region in bound PriA (PriACRR). When PriA binds to synthetic replication forks with a single-stranded lagging strand, the PriACRR is found either in a state similar to free PriA or in a rotated position that encircles the lagging strand and allows PriB recruitment. Binding to a synthetic replication fork with a duplex lagging strand neither alters the PriACRR position nor promotes PriB binding, suggesting PriA must unwind duplex lagging-strand DNA to trigger PriACRR movement and subsequent preprimosome formation. PriA variants designed to destabilize the two PriACRR positions differentially affect ATPase activity, helicase function, PriB binding in vitro, and PriA activity in vivo. These results support a regulatory switch model in which the lagging-strand DNA structure modulates the PriACRR position, thereby governing PriA's biochemical and cellular activities.
History
DepositionMar 31, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76387.png

Downloads & links

-
Map

FileDownload / File: emd_76387.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 192 pix.
= 204.288 Å		1.06 Å/pix.
x 192 pix.
= 204.288 Å		1.06 Å/pix.
x 192 pix.
= 204.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-3.1905973 - 12.566145000000001
Average (Standard dev.)0.00757839 (±0.2977635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 204.288 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_76387_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_76387_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EcPriA bound to DNA replication fork with dsDNA lagging strand

EntireName: EcPriA bound to DNA replication fork with dsDNA lagging strand
Components
  • Complex: EcPriA bound to DNA replication fork with dsDNA lagging strand
    • Protein or peptide: E. coli PriA
    • DNA: Replication fork - Leading strand template
    • DNA: Replication fork - Lagging strand template
    • DNA: Replication fork - Leading nascent strand
    • DNA: Replication fork - Lagging nascent strand

-
Supramolecule #1: EcPriA bound to DNA replication fork with dsDNA lagging strand

SupramoleculeName: EcPriA bound to DNA replication fork with dsDNA lagging strand
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 120 KDa

-
Macromolecule #1: E. coli PriA

MacromoleculeName: E. coli PriA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA 3'-5' helicase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPVAHVALPV PLPRTFDYLL PEGMTVKAGC RVRVPFGKQQ ERIGIVVSVS DASELPLNEL KAVVEVLDSE PVFTHSVWRL LLWAADYYHH PIGDVLFHAL PILLRQGRPA ANAPMWYWFA TEQGQAVDLN SLKRSPKQQQ ALAALRQGKI WREQVATLEF NDAALQALRK ...String:
MPVAHVALPV PLPRTFDYLL PEGMTVKAGC RVRVPFGKQQ ERIGIVVSVS DASELPLNEL KAVVEVLDSE PVFTHSVWRL LLWAADYYHH PIGDVLFHAL PILLRQGRPA ANAPMWYWFA TEQGQAVDLN SLKRSPKQQQ ALAALRQGKI WREQVATLEF NDAALQALRK KGLCDLASET PEFSDWRTNY AVSGERLRLN TEQATAVGAI HSAADTFSAW LLAGVTGSGK TEVYLSVLEN VLAQGKQALV MVPEIGLTPQ TIARFRERFN APVEVLHSGL NDSERLSAWL KAKNGEAAIV IGTRSALFTP FKNLGVIVID EEHDSSYKQQ EGWRYHARDL AVYRAHSEQI PIILGSATPA LETLCNVQQK KYRLLHLTRR AGNARPAIQH VLDLKGQKVQ AGLAPALITR MRQHLQANNQ VILFLNRRGF APALLCHDCG WIAECPRCDH YYTLHQAQQH LRCHHCDSQR PVPRQCPSCG STHLVPVGLG TEQLEQTLAP LFPDVPISRI DRDTTSRKGA LEQQLAEVHR GGARILIGTQ MLAKGHHFPD VTLVALLDVD GALFSADFRS AERFAQLYTQ VAGRAGRAGK QGEVVLQTHH PEHPLLQTLL YKGYDAFAEQ ALAERRMMQL PPWTSHVIVR AEDHNNQHAP LFLQQLRNLI LSSPLADDKL WVLGPVPALA PKRGGRWRWQ ILLQHPSRVR LQHIISGTLA LINTIPDSRK VKWVLDVDPI EG

UniProtKB: Replication restart protein PriA

-
Macromolecule #2: Replication fork - Leading strand template

MacromoleculeName: Replication fork - Leading strand template / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
CGAGACCGCA ATACGGATAA GGGCTGAGCA CGCCGACGAA

-
Macromolecule #3: Replication fork - Lagging strand template

MacromoleculeName: Replication fork - Lagging strand template / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
GCCGCAGACT CATTTAGCCC TTATCCGTAT TGCGGTCTCG

-
Macromolecule #4: Replication fork - Leading nascent strand

MacromoleculeName: Replication fork - Leading nascent strand / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TTCGTCGGCG TGCTC

-
Macromolecule #5: Replication fork - Lagging nascent strand

MacromoleculeName: Replication fork - Lagging nascent strand / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
AGTCTGCGGC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cisTEM / Type: NONE
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 204000
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM
Final 3D classificationSoftware - Name: cisTEM
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