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- EMDB-46797: Mycobacterium tuberculosis UvrD1: DNA-bound dimer. -

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Basic information

Entry
Database: EMDB / ID: EMD-46797
TitleMycobacterium tuberculosis UvrD1: DNA-bound dimer.
Map datasharpened map
Sample
  • Complex: UvrD1 dimer bound to dsDNA-ssDNA junction
    • Protein or peptide: ATP-dependent DNA helicase UvrD1
    • DNA: DNA (38-MER)
    • DNA: DNA (5'-D(P*GP*CP*CP*CP*TP*GP*CP*TP*GP*CP*CP*GP*AP*CP*CP*AP*AP*C)-3')
KeywordsDNA Helicase / DNA Translocase / ATPase / DNA BINDING PROTEIN / DNA BINDING 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
DepositionAug 29, 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_46797.png

Downloads & links

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Map

FileDownload / File: emd_46797.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 200 pix.
= 324.8 Å		1.62 Å/pix.
x 200 pix.
= 324.8 Å		1.62 Å/pix.
x 200 pix.
= 324.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.624 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.1055188 - 5.132851
Average (Standard dev.)-0.0008602379 (±0.0807419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 324.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_46797_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_46797_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_46797_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 dimer bound to dsDNA-ssDNA junction

EntireName: UvrD1 dimer bound to dsDNA-ssDNA junction
Components
  • Complex: UvrD1 dimer bound to dsDNA-ssDNA junction
    • Protein or peptide: ATP-dependent DNA helicase UvrD1
    • DNA: DNA (38-MER)
    • DNA: DNA (5'-D(P*GP*CP*CP*CP*TP*GP*CP*TP*GP*CP*CP*GP*AP*CP*CP*AP*AP*C)-3')

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Supramolecule #1: UvrD1 dimer bound to dsDNA-ssDNA junction

SupramoleculeName: UvrD1 dimer bound to dsDNA-ssDNA junction / 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: ATP-dependent DNA helicase UvrD1

MacromoleculeName: ATP-dependent DNA helicase UvrD1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 11.69747 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)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #3: DNA (5'-D(P*GP*CP*CP*CP*TP*GP*CP*TP*GP*CP*CP*GP*AP*CP*CP*AP*AP*C)-3')

MacromoleculeName: DNA (5'-D(P*GP*CP*CP*CP*TP*GP*CP*TP*GP*CP*CP*GP*AP*CP*CP*AP*AP*C)-3')
type: dna / ID: 3 / 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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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
SoftwareName: cryoSPARC (ver. 4.2.1)
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 49.8 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

Particle selectionNumber selected: 634557
Startup modelType of model: NONE
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: 79864
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 200 / Avg.num./class: 3500
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

a5a4


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9des:
Mycobacterium tuberculosis UvrD1: DNA-bound dimer.

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