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- EMDB-46753: Mycobacterium tuberculosis UvrD1 dimer: apo extended conformation. -

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Basic information

Entry
Database: EMDB / ID: EMD-46753
TitleMycobacterium tuberculosis UvrD1 dimer: apo extended conformation.
Map datamain map
Sample
  • Complex: Mtb UvrD1 extended dimer
    • Protein or peptide: UvrD1
KeywordsDNA Helicase / DNA Translocase / ATPase / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of strand invasion / DNA helicase complex / UV protection / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / dATP binding / ATP-dependent activity, acting on DNA / peptidoglycan-based cell wall / isomerase activity ...negative regulation of strand invasion / DNA helicase complex / UV protection / recombinational repair / 3'-5' DNA helicase activity / DNA 3'-5' helicase / dATP binding / ATP-dependent activity, acting on DNA / peptidoglycan-based cell wall / isomerase activity / double-strand break repair / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
ATP-dependent DNA helicase PcrA / PcrA/UvrD tudor domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent DNA helicase UvrD1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsChadda A / Galburt EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144282 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for dimerization and activation of UvrD-family helicases.
Authors: Ankita Chadda / Binh Nguyen / Timothy M Lohman / Eric A Galburt /
Abstract: UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single-stranded (ss) DNA ...UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single-stranded (ss) DNA but need to be activated by dimerization to unwind DNA in the absence of force or accessory factors. However, prior structural studies have only revealed monomeric complexes. Here, we report the first structures of a dimeric UvrD-family helicase, UvrD1, both free and bound to a DNA junction. In each structure, the dimer interface occurs between the 2B subdomains of each subunit. The apo UvrD1 dimer is observed in symmetric compact and extended forms indicating substantial flexibility. This symmetry is broken in the DNA-bound dimer complex with leading and trailing subunits adopting distinct conformations. Biochemical experiments reveal that the UvrD dimer shares the same 2B-2B interface. In contrast to the dimeric structures, an inactive, autoinhibited UvrD1 DNA-bound monomer structure reveals 2B subdomain-DNA contacts that are likely inhibitory. The major reorientation of the 2B subdomains that occurs upon UvrD1 dimerization prevents these duplex DNA interactions, thus relieving the autoinhibition. These structures reveal that the 2B subdomain serves a major regulatory role rather than participating directly in DNA unwinding.
History
DepositionAug 26, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46753.png

Downloads & links

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Map

FileDownload / File: emd_46753.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 200 pix.
= 329. Å		1.65 Å/pix.
x 200 pix.
= 329. Å		1.65 Å/pix.
x 200 pix.
= 329. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.658236 - 1.7215178
Average (Standard dev.)-0.0012799405 (±0.056461643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 329.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_46753_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_46753_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mtb UvrD1 extended dimer

EntireName: Mtb UvrD1 extended dimer
Components
  • Complex: Mtb UvrD1 extended dimer
    • Protein or peptide: UvrD1

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Supramolecule #1: Mtb UvrD1 extended dimer

SupramoleculeName: Mtb UvrD1 extended dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: UvrD1

MacromoleculeName: UvrD1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVHATDAKP PGPSPADQLL DGLNPQQRQA VVHEGSPLLI VAGAGSGKTA VLTRRIAYLM AARGVGVGQ ILAITFTNKA AAEMRERVVG LVGEKARYMW VSTFHSTCVR ILRNQAALIE G LNSNFSIY DADDSRRLLQ MVGRDLGLDI KRYSPRLLAN AISNLKNELI ...String:
MSVHATDAKP PGPSPADQLL DGLNPQQRQA VVHEGSPLLI VAGAGSGKTA VLTRRIAYLM AARGVGVGQ ILAITFTNKA AAEMRERVVG LVGEKARYMW VSTFHSTCVR ILRNQAALIE G LNSNFSIY DADDSRRLLQ MVGRDLGLDI KRYSPRLLAN AISNLKNELI DPHQALAGLT ED SDDLARA VASVYDEYQR RLRAANALDF DDLIGETVAV LQAFPQIAQY YRRRFRHVLV DEY QDTNHA QYVLVRELVG RDSNDGIPPG ELCVVGDADQ SIYAFRGATI RNIEDFERDY PDTR TILLE QNYRSTQNIL SAANSVIARN AGRREKRLWT DAGAGELIVG YVADNEHDEA RFVAE EIDA LAEGSEITYN DVAVFYRTNN SSRSLEEVLI RAGIPYKVVG GVRFYERKEI RDIVAY LRV LDNPGDAVSL RRILNTPRRG IGDRAEACVA VYAENTGVGF GDALVAAAQG KVPMLNT RA EKAIAGFVEM FDELRGRLDD DLGELVEAVL ERTGYRRELE ASTDPQELAR LDNLNELV S VAHEFSTDRE NAAALGPDDE DVPDTGVLAD FLERVSLVAD ADEIPEHGAG VVTLMTLHT AKGLEFPVVF VTGWEDGMFP HMRALDNPTE LSEERRLAYV GITRARQRLY VSRAIVRSSW GQPMLNPES RFLREIPQEL IDWRRTAPKP SFSAPVSGAG RFGSARPSPT RSGASRRPLL V LQVGDRVT HDKYGLGRVE EVSGVGESAM SLIDFGSSGR VKLMHNHAPV TKL

UniProtKB: ATP-dependent DNA helicase UvrD1

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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

Concentration0.38 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 4562 / Average exposure time: 9.77 sec. / Average electron dose: 46.46 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: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3lfu

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 78498
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 200 / Avg.num./class: 3500 / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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