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- EMDB-19573: RadA helicase from Streptococcus pneumoniae coordinating dsDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-19573
TitleRadA helicase from Streptococcus pneumoniae coordinating dsDNA
Map data
Sample
  • Complex: RadA helicase from Streptococcus pneumoniae coordinating dsDNA
    • Protein or peptide: DNA repair protein RadA
    • DNA: Poly-dT 30 bp
    • DNA: Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsHelicase Translocase natural transformation / DNA BINDING PROTEIN
Function / homology
Function and homology information


recombinational repair / ATP-dependent DNA damage sensor activity / damaged DNA binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
DNA repair protein RadA / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / Subunit ChlI of Mg-chelatase / AAA domain / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities ...DNA repair protein RadA / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / Subunit ChlI of Mg-chelatase / AAA domain / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RadA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsTalachia Rosa L / Fronzes R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO J / Year: 2024
Title: Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria.
Authors: Leonardo Talachia Rosa / Émeline Vernhes / Anne-Lise Soulet / Patrice Polard / Rémi Fronzes /
Abstract: Some DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly ...Some DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly conserved bacterial helicase involved in DNA repair throughout all bacterial species. In Gram-positive Firmicutes, it also has a role in natural transformation, while in Gram-negative bacteria, ComM is the canonical transformation-specific helicase. Both RadA and ComM helicases form hexameric rings and use ATP hydrolysis as an energy source to propel themselves along DNA. In this study, we present the cryoEM structures of RadA and ComM interacting with DNA and ATP analogs. These structures reveal important molecular interactions that couple ATP hydrolysis and DNA binding in RadA, as well as the role of the Lon protease-like domain, shared by RadA and ComM, in this process. Taken together, these results provide new molecular insights into the mechanisms of DNA branch migration in different pathways of homologous recombination.
History
DepositionFeb 6, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19573.png

Downloads & links

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Map

FileDownload / File: emd_19573.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 198.48 Å		0.83 Å/pix.
x 240 pix.
= 198.48 Å		0.83 Å/pix.
x 240 pix.
= 198.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.018652916 - 0.04258858
Average (Standard dev.)0.000074588075 (±0.0022265038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.48001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19573_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19573_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_19573_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : RadA helicase from Streptococcus pneumoniae coordinating dsDNA

EntireName: RadA helicase from Streptococcus pneumoniae coordinating dsDNA
Components
  • Complex: RadA helicase from Streptococcus pneumoniae coordinating dsDNA
    • Protein or peptide: DNA repair protein RadA
    • DNA: Poly-dT 30 bp
    • DNA: Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RadA helicase from Streptococcus pneumoniae coordinating dsDNA

SupramoleculeName: RadA helicase from Streptococcus pneumoniae coordinating dsDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Streptococcus pneumoniae (bacteria)

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Macromolecule #1: DNA repair protein RadA

MacromoleculeName: DNA repair protein RadA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 51.526953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASWSHPQFE KSGGGGGLVP RGSKKKATFV CQNCGYNSPK YLGRCPNCGS WSSFVEEVEV AEVKNARVSL TGEKTKPMKL AEVTSINVN RTKTEMEEFN RVLGGGVVPG SLVLIGGDPG IGKSTLLLQV STQLSQVGTV LYVSGEESAQ QIKLRAERLG D IDSEFYLY ...String:
MASWSHPQFE KSGGGGGLVP RGSKKKATFV CQNCGYNSPK YLGRCPNCGS WSSFVEEVEV AEVKNARVSL TGEKTKPMKL AEVTSINVN RTKTEMEEFN RVLGGGVVPG SLVLIGGDPG IGKSTLLLQV STQLSQVGTV LYVSGEESAQ QIKLRAERLG D IDSEFYLY AETNMQSVRA EVERIQPDFL IIDSIQTIMS PEISGVQGSV SQVREVTAEL MQLAKTNNIA IFIVGHVTKE GT LAGPRML EHMVDTVLYF EGERHHTFRI LRAVKNRFGS TNEIGIFEMQ SGGLVEVLNP SQVFLEERLD GATGSSIVVT MEG TRPILA EVQALVTPTM FGNAKRTTTG LDFNRASLIM AVLEKRAGLL LQNQDAYLKS AGGVKLDEPA IDLAVAVAIA SSYK DKPTN PQECFVGELG LTGEIRRVNR IEQRINEAAK LGFTKIYVPK NSLTGITLPK EIQVIGVTTI QEVLKKVF

UniProtKB: DNA repair protein RadA

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Macromolecule #2: Poly-dT 30 bp

MacromoleculeName: Poly-dT 30 bp / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.080827 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)

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Macromolecule #3: Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp)

MacromoleculeName: Poly-dA (30 bp) Poly-dC (60 bp) Poly-dA (30 bp) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 36.098395 KDa
SequenceString: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC) (DC)(DC)(DC)(DC)(DC)(DC) ...String:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III
Details0.35 mg/ml protein and 100 uM of hybrid DNA

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 54.04 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

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Image processing

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

5lkm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 303651
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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