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- EMDB-34154: Structure of lambda repressor in complex with RecA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-34154
TitleStructure of lambda repressor in complex with RecA filament
Map data
Sample
  • Complex: RecA-CI complex
    • Protein or peptide: Repressor protein cI
    • Protein or peptide: Protein RecA
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsSOS response / RecA / lambda repressor / Filament / DNA repair / Helical reconstruction / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


maintenance of viral latency / DNA polymerase V complex / latency-replication decision / positive regulation of viral transcription / homologous recombination / negative regulation of transcription by competitive promoter binding / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation ...maintenance of viral latency / DNA polymerase V complex / latency-replication decision / positive regulation of viral transcription / homologous recombination / negative regulation of transcription by competitive promoter binding / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / ATP-dependent activity, acting on DNA / translesion synthesis / core promoter sequence-specific DNA binding / cell motility / single-stranded DNA binding / DNA recombination / DNA-binding transcription factor binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. ...: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / RecA N-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / 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. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Repressor protein cI / Protein RecA
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus) / Escherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 2.78 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-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34154.png

Downloads & links

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Map

FileDownload / File: emd_34154.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 220 pix.
= 261.8 Å		1.19 Å/pix.
x 220 pix.
= 261.8 Å		1.19 Å/pix.
x 220 pix.
= 261.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.19674052 - 0.37157422
Average (Standard dev.)0.00025339844 (±0.008748681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 261.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34154_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34154_half_map_2.map
Projections & Slices
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Sample components

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Entire : RecA-CI complex

EntireName: RecA-CI complex
Components
  • Complex: RecA-CI complex
    • Protein or peptide: Repressor protein cI
    • Protein or peptide: Protein RecA
    • 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-CI complex

SupramoleculeName: RecA-CI complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia phage Lambda (virus)

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Macromolecule #1: Repressor protein cI

MacromoleculeName: Repressor protein cI / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 14.999833 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEF TFAKLIRDSG QVFLQPLNPQ YPMIPCNESC SVVGKVIASQ WPEETFG

UniProtKB: Repressor protein cI

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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

UniProtKB: Protein RecA

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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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 31.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 118.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 500031
Startup modelType of model: EMDB MAP
EMDB ID:

22524

Final angle assignmentType: NOT APPLICABLE

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