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- EMDB-51673: C. thermocellum UvrA in complex with DNA with a fluorescein modif... -

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Basic information

Entry
Database: EMDB / ID: EMD-51673
TitleC. thermocellum UvrA in complex with DNA with a fluorescein modification (basal conformation)
Map dataMap sharpened locally with LocScale2
Sample
  • Complex: C. thermocellum UvrA in complex with DNA with a fluorescein modification
    • Protein or peptide: UvrABC system protein A
    • DNA: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
  • Ligand: ZINC ION
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
UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein A
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 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
DepositionSep 30, 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_51673.png

Downloads & links

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Map

FileDownload / File: emd_51673.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened locally with LocScale2
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4129718 - 0.8560205
Average (Standard dev.)0.002368065 (±0.023668345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51673_msk_1.map
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Mask #2

Fileemd_51673_msk_2.map
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Additional map: Unsharpened map

Fileemd_51673_additional_1.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_51673_half_map_1.map
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Half map: #1

Fileemd_51673_half_map_2.map
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Sample components

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

EntireName: C. thermocellum UvrA in complex with DNA with a fluorescein modification
Components
  • Complex: C. thermocellum UvrA in complex with DNA with a fluorescein modification
    • Protein or peptide: UvrABC system protein A
    • DNA: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
  • Ligand: ZINC ION

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

SupramoleculeName: C. thermocellum UvrA in complex with DNA with a fluorescein modification
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 245 KDa

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Macromolecule #1: UvrABC system protein A

MacromoleculeName: UvrABC system protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Molecular weightTheoretical: 107.144773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKKDYIVVKG AREHNLKNID VKIPRDKFVV ITGLSGSGKS SLAFDTIYAE GQRRYVESLS SYARQFLGQ MEKPDVDYID GLSPAIAIDQ KTTSRNPRST VGTVTEIYDY LRLLFARIGT PHCYLCGREI SQQTVDQMVD R IMEFEEGT ...String:
MGSSHHHHHH SSGLVPRGSH MKKDYIVVKG AREHNLKNID VKIPRDKFVV ITGLSGSGKS SLAFDTIYAE GQRRYVESLS SYARQFLGQ MEKPDVDYID GLSPAIAIDQ KTTSRNPRST VGTVTEIYDY LRLLFARIGT PHCYLCGREI SQQTVDQMVD R IMEFEEGT RIQLLAPVVR GRKGEYHKLI EDIKKEGYVR IRVDGEVVDV NDPVNLDKNK KHNIEIVVDR LIVRPGIQKR LT DSIETVL RLSNGILVVD VIGGKEMLLS QNFACTECNV SMEEITPRMF SFNNPYGACP ECTGLGSLMR IDPDLVIPDK KLS LAQGAV RASGWNIAND ESYARMYIDA LAKHYNFSVD TPVEELPPHI LDIILYGTNG EKIKIEYERE NEKGTFMASF PGII NSMER RYKETTSEVM KQYYENFMSN IPCPVCKGAR LKKESLAVTI GGKNIYEVCC LSIGEAKEFF ANLNLTERQQ LIARQ ILKE INARLGFLVD VGLDYLTLAR AAGTLSGGEA QRIRLATQIG SGLMGVIYIL DEPSIGLHQR DNDRLLRSLK KLRDLG NTL LVVEHDEDTM YASDYIIDLG PGAGSHGGQI VAEGTVEEIK QNPNSVTGEY LSGRKKIEVP KERRKPNGKW LEIIGAR EN NLKNINVRIP LGVFTCITGV SGSGKSSLIN EILYKRLAAE LNRASVKPGE HDLIKGIEYL DKVIDIDQSP IGRTPRSN P ATYTGVFDFI REIFANTTEA KTRGYKAGRF SFNVKGGRCE ACAGDGINKI EMHFLPDIYV PCEVCKGKRY NRETLEVRY KGKNIAEVLD MTVEEALEFF KNIPRIHKKI ETLYDVGLGY IKLGQSSTTL SGGEAQRVKL ATELSRKSTG KTMYILDEPT TGLHMADVH RLVGILHRLV EAGNSVVVIE HNLDVIKTAD YIIDLGPEGG SGGGLVVAEG TPEEVAKVEN SYTGQFLKKV L ST

UniProtKB: UvrABC system protein A

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Macromolecule #2: DNA (50-MER) with a fluorescein modification - (random sequence b...

MacromoleculeName: DNA (50-MER) with a fluorescein modification - (random sequence built in model)
type: dna / ID: 2 / Details: Random sequence built in model. / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.411887 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT) (DG)(DT)(DT)(DA)(DC)(DG)(DG)(DC)(DT)(DC) (DC)(DA)(DT)(DC)(DA)(DG)(DA)(DT)(DG) (DG)(DA)(DG)(DC)(DC)(DG)(DT)(DA)(DA)(DC) (DA) (DG)(DT)(DA)(DC)(DG)(DA)(DT)(DG) (DC)(DA)

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample fixed with 0.01% 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
SoftwareName: EPU (ver. 2.10.0.1941REL)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3012 / Average electron dose: 41.64 e/Å2 / Details: 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: 1.9000000000000001 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 770286
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-intio model
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 346137
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9gxs:
C. thermocellum UvrA in complex with DNA with a fluorescein modification (basal conformation)

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