[English] 日本語
Yorodumi
- EMDB-34153: Structure of UmuD in complex with RecA filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34153
TitleStructure of UmuD in complex with RecA filament
Map data
Sample
  • Complex: RecA-UmuD complex
    • Protein or peptide: DNA polymerase V subunit UmuD
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: Protein RecA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Function / homology
Function and homology information


repressor LexA / SOS response / ATP-dependent DNA damage sensor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity ...repressor LexA / SOS response / ATP-dependent DNA damage sensor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / DNA repair / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Peptidase S24, LexA-like / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal ...Peptidase S24, LexA-like / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / : / : / 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 polymerase V subunit UmuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.31 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

-
Structure visualization

Supplemental images

emd_34153.png

Downloads & links

-
Map

FileDownload / File: emd_34153.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.19 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.07008572 - 0.113613494
Average (Standard dev.)0.00011856183 (±0.0032810997)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_34153_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34153_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34153_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RecA-UmuD complex

EntireName: RecA-UmuD complex
Components
  • Complex: RecA-UmuD complex
    • Protein or peptide: DNA polymerase V subunit UmuD
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: Protein RecA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: RecA-UmuD complex

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

-
Macromolecule #1: DNA polymerase V subunit UmuD

MacromoleculeName: DNA polymerase V subunit UmuD / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: repressor LexA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.017207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLFIKPADLR EIVTFPLFSD LVQCGFPSPA ADYVEQRIDL NQLLIQHPSA TYFVKASGDS MIDGGISDGD LLIVDSAITA SHGDIVIAA VDGEFTVAKL QLRPTVQLIP MNSAYSPITI SSEDTLDVFG VVIHVVKAMR

-
Macromolecule #3: Protein RecA

MacromoleculeName: Protein RecA / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #2: 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: 2 / 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)

-
Macromolecule #4: MAGNESIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 1.7 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

22524

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 31.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 118.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137040

+
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