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- EMDB-46850: Mycobacterium tuberculosis UvrD1 monomer-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-46850
TitleMycobacterium tuberculosis UvrD1 monomer-DNA complex
Map dataMycobacterium tuberculosis UvrD1 monomer-DNA complex
Sample
  • Complex: UvrD1 monomer-DNA junction complex
    • Protein or peptide: ATP-dependent DNA helicase UvrD1
    • DNA: DNA (18-MER)
    • DNA: DNA (28-MER)
KeywordsDNA Helicase / DNA Translocase / ATPase / MOTOR PROTEIN / MOTOR PROTEIN-DNA complex
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
DepositionSep 3, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46850.png

Downloads & links

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Map

FileDownload / File: emd_46850.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium tuberculosis UvrD1 monomer-DNA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 280 pix.
= 243.04 Å		0.87 Å/pix.
x 280 pix.
= 243.04 Å		0.87 Å/pix.
x 280 pix.
= 243.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.22397776 - 0.46573642
Average (Standard dev.)0.00013584315 (±0.019872312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 243.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_46850_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_46850_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_46850_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : UvrD1 monomer-DNA junction complex

EntireName: UvrD1 monomer-DNA junction complex
Components
  • Complex: UvrD1 monomer-DNA junction complex
    • Protein or peptide: ATP-dependent DNA helicase UvrD1
    • DNA: DNA (18-MER)
    • DNA: DNA (28-MER)

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Supramolecule #1: UvrD1 monomer-DNA junction complex

SupramoleculeName: UvrD1 monomer-DNA junction complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: ATP-dependent DNA helicase UvrD1

MacromoleculeName: ATP-dependent DNA helicase UvrD1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA 3'-5' helicase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 85.154898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVHATDAKP PGPSPADQLL DGLNPQQRQA VVHEGSPLLI VAGAGSGKTA VLTRRIAYLM AARGVGVGQI LAITFTNKAA AEMRERVVG LVGEKARYMW VSTFHSTCVR ILRNQAALIE GLNSNFSIYD ADDSRRLLQM VGRDLGLDIK RYSPRLLANA I SNLKNELI ...String:
MSVHATDAKP PGPSPADQLL DGLNPQQRQA VVHEGSPLLI VAGAGSGKTA VLTRRIAYLM AARGVGVGQI LAITFTNKAA AEMRERVVG LVGEKARYMW VSTFHSTCVR ILRNQAALIE GLNSNFSIYD ADDSRRLLQM VGRDLGLDIK RYSPRLLANA I SNLKNELI DPHQALAGLT EDSDDLARAV ASVYDEYQRR LRAANALDFD DLIGETVAVL QAFPQIAQYY RRRFRHVLVD EY QDTNHAQ YVLVRELVGR DSNDGIPPGE LCVVGDADQS IYAFRGATIR NIEDFERDYP DTRTILLEQN YRSTQNILSA ANS VIARNA GRREKRLWTD AGAGELIVGY VADNEHDEAR FVAEEIDALA EGSEITYNDV AVFYRTNNSS RSLEEVLIRA GIPY KVVGG VRFYERKEIR DIVAYLRVLD NPGDAVSLRR ILNTPRRGIG DRAEACVAVY AENTGVGFGD ALVAAAQGKV PMLNT RAEK AIAGFVEMFD ELRGRLDDDL GELVEAVLER TGYRRELEAS TDPQELARLD NLNELVSVAH EFSTDRENAA ALGPDD EDV PDTGVLADFL ERVSLVADAD EIPEHGAGVV TLMTLHTAKG LEFPVVFVTG WEDGMFPHMR ALDNPTELSE ERRLAYV GI TRARQRLYVS RAIVRSSWGQ PMLNPESRFL REIPQELIDW RRTAPKPSFS APVSGAGRFG SARPSPTRSG ASRRPLLV L QVGDRVTHDK YGLGRVEEVS GVGESAMSLI DFGSSGRVKL MHNHAPVTKL

UniProtKB: ATP-dependent DNA helicase UvrD1

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Macromolecule #2: DNA (18-MER)

MacromoleculeName: DNA (18-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 5.422508 KDa
SequenceString:
(DG)(DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG)(DC) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DC)

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Macromolecule #3: DNA (28-MER)

MacromoleculeName: DNA (28-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 8.655542 KDa
SequenceString:
(DG)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DG)(DC) (DA)(DG)(DC)(DA)(DG)(DG)(DG)(DC)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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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: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 82.0 K / Max: 84.0 K
Specialist opticsSpherical aberration corrector: Microscope is outfitted with a Cs image corrector with two hexapole elements
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 4999 / Average exposure time: 7.27 sec. / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 713562
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282302
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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