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- EMDB-4958: Negative stain EM 3D reconstruction of the UvrA-UvrB-DNA complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-4958
TitleNegative stain EM 3D reconstruction of the UvrA-UvrB-DNA complex.
Map dataNegative stain EM 3D reconstruction of UvrA-UvrB-DNA complex.
Sample
  • Complex: UvrA-UvrB-DNA complex.
Biological speciesThermotoga maritima (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsSwuec P / Renault L / Costa A
Funding support Poland, United Kingdom, 4 items
OrganizationGrant numberCountry
European Research Council81500 and 261351 Poland
Medical Research Council (United Kingdom)FC001065 United Kingdom
Cancer Research UKFC001065 United Kingdom
Wellcome TrustFC001065 United Kingdom
CitationJournal: DNA Repair (Amst) / Year: 2020
Title: A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair.
Authors: Marcin Jaciuk / Paolo Swuec / Vineet Gaur / Joanna M Kasprzak / Ludovic Renault / Mateusz Dobrychłop / Shivlee Nirwal / Janusz M Bujnicki / Alessandro Costa / Marcin Nowotny /
Abstract: Nucleotide excision repair (NER) is a DNA repair pathway present in all domains of life. In bacteria, UvrA protein localizes the DNA lesion, followed by verification by UvrB helicase and excision by ...Nucleotide excision repair (NER) is a DNA repair pathway present in all domains of life. In bacteria, UvrA protein localizes the DNA lesion, followed by verification by UvrB helicase and excision by UvrC double nuclease. UvrA senses deformations and flexibility of the DNA duplex without precisely localizing the lesion in the damaged strand, an element essential for proper NER. Using a combination of techniques, we elucidate the mechanism of the damage verification step in bacterial NER. UvrA dimer recruits two UvrB molecules to its two sides. Each of the two UvrB molecules clamps a different DNA strand using its β-hairpin element. Both UvrB molecules then translocate to the lesion, and UvrA dissociates. The UvrB molecule that clamps the damaged strand gets stalled at the lesion to recruit UvrC. This mechanism allows UvrB to verify the DNA damage and identify its precise location triggering subsequent steps in the NER pathway.
History
DepositionMay 9, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseMay 22, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4958.png

Downloads & links

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Map

FileDownload / File: emd_4958.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM 3D reconstruction of UvrA-UvrB-DNA complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.73 Å/pix.
x 168 pix.
= 458.64 Å		2.73 Å/pix.
x 168 pix.
= 458.64 Å		2.73 Å/pix.
x 168 pix.
= 458.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0285 / Movie #1: 0.0285
Minimum - Maximum-0.05472279 - 0.078293614
Average (Standard dev.)-0.00041212118 (±0.005489853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 458.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z458.640458.640458.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0550.078-0.000

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Supplemental data

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Sample components

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Entire : UvrA-UvrB-DNA complex.

EntireName: UvrA-UvrB-DNA complex.
Components
  • Complex: UvrA-UvrB-DNA complex.

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Supramolecule #1: UvrA-UvrB-DNA complex.

SupramoleculeName: UvrA-UvrB-DNA complex. / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermotoga maritima (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 2100
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 23547
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)

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