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- EMDB-51690: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-51690
TitleC. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP: focused map
Map dataGlobally sharpened map with the beta factor of -122.3
Sample
  • Complex: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
    • Complex: C. thermocellum UvrA-UvrB
      • Protein or peptide: UvrABC system protein A
      • Protein or peptide: UvrABC system protein B
    • Complex: DNA with a fluorescein modification and AMPPNP
      • DNA: DNA (50-MER) with a fluorescein modification
KeywordsDNA binding protein / DNA Repair pathway / Nucleotide excision repair pathway / NER
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrA, interaction domain / UvrB/uvrC motif / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain ...UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrA, interaction domain / UvrB/uvrC motif / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / UvrB, interaction domain / UvrB interaction domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / Helicase conserved C-terminal domain / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein B / UvrABC system protein A
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsNirwal S / Czarnocki-Cieciura M / Nowotny M
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/A/NZ1/01098 Poland
CitationJournal: Nat Commun / Year: 2025
Title: Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.
Authors: Shivlee Nirwal / Mariusz Czarnocki-Cieciura / Weronika Zajko / Krzysztof Skowronek / Roman H Szczepanowski / Marcin Nowotny /
Abstract: Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two ...Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two adenosine triphosphatase modules and forms dimers. The DNA is handed over from UvrA to UvrB, which is a weak helicase that verifies the presence of damage. Despite intense studies, the role of the ATPase activity of UvrA in damage recognition is unclear. Here, we present a series of cryo-electron microscopy structures of UvrA in complex with three different DNAs and in the presence and absence of nucleotides. We also present a structure of UvrA:UvrB:DNA complex. These structures reveal a major rearrangement of the UvrA dimer upon ATP binding. We propose that these conformational changes are used to mechanically probe the integrity of DNA for damage localization. Collectively, our results present snapshots of UvrA's ATP-dependent DNA damage detection.
History
DepositionOct 1, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51690.png

Downloads & links

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Map

FileDownload / File: emd_51690.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened map with the beta factor of -122.3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.1762271 - 1.959269
Average (Standard dev.)0.0018782483 (±0.04806802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51690_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Mask #2

Fileemd_51690_msk_2.map
Projections & Slices
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Additional map: Unsharpened map

Fileemd_51690_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_51690_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_51690_half_map_2.map
Projections & Slices
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Sample components

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Entire : C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein ...

EntireName: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
Components
  • Complex: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
    • Complex: C. thermocellum UvrA-UvrB
      • Protein or peptide: UvrABC system protein A
      • Protein or peptide: UvrABC system protein B
    • Complex: DNA with a fluorescein modification and AMPPNP
      • DNA: DNA (50-MER) with a fluorescein modification

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Supramolecule #1: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein ...

SupramoleculeName: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 398 KDa

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Supramolecule #2: C. thermocellum UvrA-UvrB

SupramoleculeName: C. thermocellum UvrA-UvrB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Acetivibrio thermocellus (bacteria)

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Supramolecule #3: DNA with a fluorescein modification and AMPPNP

SupramoleculeName: DNA with a fluorescein modification and AMPPNP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: UvrABC system protein A

MacromoleculeName: UvrABC system protein A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKKDYIVVK GAREHNLKNI DVKIPRDKFV VITGLSGSGK SSLAFDTIYA EGQRRYVESL SSYARQFLGQ M EKPDVDYI DGLSPAIAID QKTTSRNPRS TVGTVTEIYD YLRLLFARIG TPHCYLCGRE ISQQTVDQMV DR IMEFEEG ...String:
MGSSHHHHHH SSGLVPRGSH MKKDYIVVK GAREHNLKNI DVKIPRDKFV VITGLSGSGK SSLAFDTIYA EGQRRYVESL SSYARQFLGQ M EKPDVDYI DGLSPAIAID QKTTSRNPRS TVGTVTEIYD YLRLLFARIG TPHCYLCGRE ISQQTVDQMV DR IMEFEEG TRIQLLAPVV RGRKGEYHKL IEDIKKEGYV RIRVDGEVVD VNDPVNLDKN KKHNIEIVVD RLI VRPGIQ KRLTDSIETV LRLSNGILVV DVIGGKEMLL SQNFACTECN VSMEEITPRM FSFNNPYGAC PECT GLGSL MRIDPDLVIP DKKLSLAQGA VRASGWNIAN DESYARMYID ALAKHYNFSV DTPVEELPPH ILDII LYGT NGEKIKIEYE RENEKGTFMA SFPGIINSME RRYKETTSEV MKQYYENFMS NIPCPVCKGA RLKKES LAV TIGGKNIYEV CCLSIGEAKE FFANLNLTER QQLIARQILK EINARLGFLV DVGLDYLTLA RAAGTLS GG EAQRIRLATQ IGSGLMGVIY ILDEPSIGLH QRDNDRLLRS LKKLRDLGNT LLVVEHDEDT MYASDYII D LGPGAGSHGG QIVAEGTVEE IKQNPNSVTG EYLSGRKKIE VPKERRKPNG KWLEIIGARE NNLKNINVR IPLGVFTCIT GVSGSGKSSL INEILYKRLA AELNRASVKP GEHDLIKGIE YLDKVIDIDQ SPIGRTPRSN PATYTGVFD FIREIFANTT EAKTRGYKAG RFSFNVKGGR CEACAGDGIN KIEMHFLPDI YVPCEVCKGK R YNRETLEV RYKGKNIAEV LDMTVEEALE FFKNIPRIHK KIETLYDVGL GYIKLGQSST TLSGGEAQRV KL ATELSRK STGKTMYILD EPTTGLHMAD VHRLVGILHR LVEAGNSVVV IEHNLDVIKT ADYIIDLGPE GGS GGGLVV AEGTPEEVAK VENSYTGQFL KKVLST

UniProtKB: UvrABC system protein A

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Macromolecule #2: UvrABC system protein B

MacromoleculeName: UvrABC system protein B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMHKFKLVSD YKPCGDQPEA IDKLVEGINR GYRGQTLLGV TGSGKTFTMA NVIERVQKPT LVIAHNKTLA A QLCSEFKE FFPNNCVEYF VSYYDYYQPE AYIPATDTYI EKDSSINDEI DKLRHSATAA LFERRDVIIV AS VSCIYGL GDPEDYTDLM LSLRPGMIKD ...String:
SMHKFKLVSD YKPCGDQPEA IDKLVEGINR GYRGQTLLGV TGSGKTFTMA NVIERVQKPT LVIAHNKTLA A QLCSEFKE FFPNNCVEYF VSYYDYYQPE AYIPATDTYI EKDSSINDEI DKLRHSATAA LFERRDVIIV AS VSCIYGL GDPEDYTDLM LSLRPGMIKD RDEIIRKLVD IQYERNEIDF KRGKFRVRGD ILEIFPASSS DKV IRVEFF GEEIDRITEV DSLTGEITGV CSHVAIFPAS HYATTKAKMQ RAIASIEQEL EERVRELKSQ GKLL EAQRL EQRTRYDLEM MQEIGFCQGI ENYSRHISGR APGSPPFTLI DYFPKDFLLI IDESHVTIPQ IGAMY NGDR SRKESLVEYG FRLPSAFDNR PLTFEEFEKK INQVIFVSAT PAKYEREHSQ QIVEQIIRPT GLLDPE IVV KPVKGQIDDL IGEISERVQK NQRVMITTLT KKMAEDLTDY LRELDFKVEY LHSDIDTIER MEIIRNL RL GVFDVLVGIN LLREGLDIPE VSLVAILDAD KEGFLRSETS LIQTIGRAAR NVEGKVIMYA DTITDSMR R AIDETNRRRK IQSEYNQKHG ITPKSVQKGI RDVIEITKVA EEDAKYFIRG DEDSMDKDEV LDLIEKLTN EMKAAAAELQ FERAAELRDK IAELKKKIGA

UniProtKB: UvrABC system protein B

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Macromolecule #3: DNA (50-MER) with a fluorescein modification

MacromoleculeName: DNA (50-MER) with a fluorescein modification / type: dna / ID: 3 / Details: Random sequence built in model. / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
GC ATC GTA CTG TTA C GG CTC CAT CAG ATG G AG CCG TAA CAG TAC G AT GCA

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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

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample fixed by GraFix with 0.1% glutaraldehyde and concentrated prior to vitrification; exact concentration cannot be estimated accurately.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9695 / Average electron dose: 40.73 e/Å2 / Details: 6326 images were collected with 30 deg stage tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2702429
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-intio model in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 136850
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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