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- EMDB-34151: Structure of DinI in complex with RecA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-34151
TitleStructure of DinI in complex with RecA filament
Map data
Sample
  • Complex: RecA-DinI complex
    • Complex: RecA-DinI
      • Protein or peptide: DNA damage-inducible protein I
      • Protein or peptide: Protein RecA
    • Complex: DNA
      • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Function / homology
Function and homology information


ATP-dependent DNA damage sensor activity / SOS response / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / enzyme binding / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
DNA damage-inducible protein DinI-like / DinI-like superfamily / DinI-like family / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA ...DNA damage-inducible protein DinI-like / DinI-like superfamily / DinI-like family / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein RecA / DNA damage-inducible protein I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsGao B / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970040 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis for regulation of SOS response in bacteria.
Authors: Bo Gao / Liang Liang / Lu Su / Aijia Wen / Chun Zhou / Yu Feng /
Abstract: In response to DNA damage, bacterial RecA protein forms filaments with the assistance of DinI protein. The RecA filaments stimulate the autocleavage of LexA, the repressor of more than 50 SOS genes, ...In response to DNA damage, bacterial RecA protein forms filaments with the assistance of DinI protein. The RecA filaments stimulate the autocleavage of LexA, the repressor of more than 50 SOS genes, and activate the SOS response. During the late phase of SOS response, the RecA filaments stimulate the autocleavage of UmuD and λ repressor CI, leading to mutagenic repair and lytic cycle, respectively. Here, we determined the cryo-electron microscopy structures of RecA filaments in complex with DinI, LexA, UmuD, and λCI by helical reconstruction. The structures reveal that LexA and UmuD dimers bind in the filament groove and cleave in an intramolecular and an intermolecular manner, respectively, while λCI binds deeply in the filament groove as a monomer. Despite their distinct folds and oligomeric states, all RecA filament binders recognize the same conserved protein features in the filament groove. The SOS response in bacteria can lead to mutagenesis and antimicrobial resistance, and our study paves the way for rational drug design targeting the bacterial SOS response.
History
DepositionAug 22, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34151.png

Downloads & links

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Map

FileDownload / File: emd_34151.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.05300864 - 0.08180585
Average (Standard dev.)0.00010452483 (±0.0028403145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34151_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34151_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RecA-DinI complex

EntireName: RecA-DinI complex
Components
  • Complex: RecA-DinI complex
    • Complex: RecA-DinI
      • Protein or peptide: DNA damage-inducible protein I
      • Protein or peptide: Protein RecA
    • Complex: DNA
      • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: RecA-DinI complex

SupramoleculeName: RecA-DinI complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: RecA-DinI

SupramoleculeName: RecA-DinI / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: DNA damage-inducible protein I

MacromoleculeName: DNA damage-inducible protein I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 8.957937 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRIEVTIAKT SPLPAGAIDA LAGELSRRIQ YAFPDNEGHV SVRYAAANNL SVIGATKEDK QRISEILQET WESADDWFVS E

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Macromolecule #2: Protein RecA

MacromoleculeName: Protein RecA / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.016277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAIDENKQKA LAAALGQIEK QFGKGSIMRL GEDRSMDVET ISTGSLSLDI ALGAGGLPMG RIVEIYGPES SGKTTLTLQV IAAAQREGK TCAFIDAEHA LDPIYARKLG VDIDNLLCSQ PDTGEQALEI CDALARSGAV DVIVVDSVAA LTPKAEIEGE I GDSHMGLA ...String:
MAIDENKQKA LAAALGQIEK QFGKGSIMRL GEDRSMDVET ISTGSLSLDI ALGAGGLPMG RIVEIYGPES SGKTTLTLQV IAAAQREGK TCAFIDAEHA LDPIYARKLG VDIDNLLCSQ PDTGEQALEI CDALARSGAV DVIVVDSVAA LTPKAEIEGE I GDSHMGLA ARMMSQAMRK LAGNLKQSNT LLIFINQIRM KIGVMFGNPE TTTGGNALKF YASVRLDIRR IGAVKEGENV VG SETRVKV VKNKIAAPFK QAEFQILYGE GINFYGELVD LGVKEKLIEK AGAWYSYKGE KIGQGKANAT AWLKDNPETA KEI EKKVRE LLLSNPNSTP DFSVDDSEGV AETNEDF

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Macromolecule #3: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.780199 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

22524

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 31.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 118.0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40451

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