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- EMDB-51169: MtUvrA2 dimer empty -

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Basic information

Entry
Database: EMDB / ID: EMD-51169
TitleMtUvrA2 dimer empty
Map data
Sample
  • Complex: MtUvrA2 alone
    • Protein or peptide: UvrABC system protein A
  • Ligand: ZINC ION
KeywordsDNA repair / NER / UVRA / UVRB / UVR / MTB / DNA BINDING PROTEIN
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 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsGenta M / Capelli R / Ferrara G / Rizzi M / Rossi F / Jeruzalmi D / Bolognesi M / Chaves-Sanjuan A / Miggiano R
Funding support Italy, 1 items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaP2022P8KMF Italy
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair.
Authors: Marianna Genta / Giulia Ferrara / Riccardo Capelli / Diego Rondelli / Sarah Sertic / Martino Bolognesi / Menico Rizzi / Franca Rossi / David Jeruzalmi / Antonio Chaves-Sanjuan / Riccardo Miggiano /
Abstract: Nucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are ...Nucleotide excision repair (NER) represents one of the major molecular machineries that control chromosome stability in all living species. In Eubacteria, the initial stages of the repair process are carried out by the UvrABC excinuclease complex. Despite the wealth of structural data available, some crucial details of the pathway remain elusive. In this study, we present a structural investigation of the Mycobacterium tuberculosis UvrAUvrB complex and of the UvrA dimer, both in complex with damaged DNA. Our analyses yield insights into the DNA binding mode of UvrA, showing an unexplored conformation of Insertion Domains (IDs), underlying the essential role of these domains in DNA coordination. Furthermore, we observe an interplay between the ID and the UvrB Binding Domain (UBD): after the recognition of the damage, the IDs repositions with the concomitant reorganization of UBD, allowing the formation of the complex between UvrA and UvrB. These events are detected along the formation of the uncharacterized UvrAUvrB-DNA and the UvrAUvrB-DNA complexes which we interpret as hierarchical steps initiating the DNA repair cascade in the NER pathway, resulting in the formation of the pre-incision complex.
History
DepositionJul 26, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51169.png

Downloads & links

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Map

FileDownload / File: emd_51169.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.23923272 - 1.1771424
Average (Standard dev.)-0.0003633408 (±0.03751587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 355.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51169_msk_1.map
Projections & Slices
AxesZYX

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Additional map: sharp

Fileemd_51169_additional_1.map
Annotationsharp
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Half map: #2

Fileemd_51169_half_map_1.map
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Half map: #1

Fileemd_51169_half_map_2.map
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Sample components

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Entire : MtUvrA2 alone

EntireName: MtUvrA2 alone
Components
  • Complex: MtUvrA2 alone
    • Protein or peptide: UvrABC system protein A
  • Ligand: ZINC ION

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Supramolecule #1: MtUvrA2 alone

SupramoleculeName: MtUvrA2 alone / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 220 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: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 108.806398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMADRLIVKG AREHNLRSVD LDLPRDALIV FTGLSGSGKS SLAFDTIFAE GQRRYVESLS AYARQFLGQ MDKPDVDFIE GLSPAVSIDQ KSTNRNPRST VGTITEVYDY LRLLYARAGT PHCPTCGERV ARQTPQQIVD Q VLAMPEGT ...String:
MGHHHHHHHH HHSSGHIEGR HMADRLIVKG AREHNLRSVD LDLPRDALIV FTGLSGSGKS SLAFDTIFAE GQRRYVESLS AYARQFLGQ MDKPDVDFIE GLSPAVSIDQ KSTNRNPRST VGTITEVYDY LRLLYARAGT PHCPTCGERV ARQTPQQIVD Q VLAMPEGT RFLVLAPVVR TRKGEFADLF DKLNAQGYSR VRVDGVVHPL TDPPKLKKQE KHDIEVVVDR LTVKAAAKRR LT DSVETAL NLADGIVVLE FVDHELGAPH REQRFSEKLA CPNGHALAVD DLEPRSFSFN SPYGACPECS GLGIRKEVDP ELV VPDPDR TLAQGAVAPW SNGHTAEYFT RMMAGLGEAL GFDVDTPWRK LPAKARKAIL EGADEQVHVR YRNRYGRTRS YYAD FEGVL AFLQRKMSQT ESEQMKERYE GFMRDVPCPV CAGTRLKPEI LAVTLAGESK GEHGAKSIAE VCELSIADCA DFLNA LTLG PREQAIAGQV LKEIRSRLGF LLDVGLEYLS LSRAAATLSG GEAQRIRLAT QIGSGLVGVL YVLDEPSIGL HQRDNR RLI ETLTRLRDLG NTLIVVEHDE DTIEHADWIV DIGPGAGEHG GRIVHSGPYD ELLRNKDSIT GAYLSGRESI EIPAIRR SV DPRRQLTVVG AREHNLRGID VSFPLGVLTS VTGVSGSGKS TLVNDILAAV LANRLNGARQ VPGRHTRVTG LDYLDKLV R VDQSPIGRTP RSNPATYTGV FDKIRTLFAA TTEAKVRGYQ PGRFSFNVKG GRCEACTGDG TIKIEMNFLP DVYVPCEVC QGARYNRETL EVHYKGKTVS EVLDMSIEEA AEFFEPIAGV HRYLRTLVDV GLGYVRLGQP APTLSGGEAQ RVKLASELQK RSTGRTVYI LDEPTTGLHF DDIRKLLNVI NGLVDKGNTV IVIEHNLDVI KTSDWIIDLG PEGGAGGGTV VAQGTPEDVA A VPASYTGK FLAEVVGGGA SAATSRSNRR RNVSA

UniProtKB: UvrABC system protein A

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 3 / 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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMNaClNaCl
20.0 mMTris HCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3642 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 240304
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 26736
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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