[English] 日本語
Yorodumi
- EMDB-46799: Mycobacterium tuberculosis UvrD1 dimer: DNA-bound dimer, dsDNA ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46799
TitleMycobacterium tuberculosis UvrD1 dimer: DNA-bound dimer, dsDNA masked map
Map dataSharpened masked map. dsDNA was masked to obtain higher resolution of the protein and bound ssDNA in the core of the complex. See related entries.
Sample
  • Complex: UvrD1 dimer bound to dsDNA-ssDNA junction
    • Protein or peptide: UvrD1
    • DNA: DNA strand
    • DNA: DNA
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 / dATP binding / DNA 3'-5' helicase / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / peptidoglycan-based cell wall / double-strand break repair ...negative regulation of strand invasion / DNA helicase complex / UV protection / recombinational repair / dATP binding / DNA 3'-5' helicase / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / peptidoglycan-based cell wall / double-strand break repair / DNA replication / 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: 6.4 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

-
Structure visualization

Supplemental images

emd_46799.png

Downloads & links

-
Map

FileDownload / File: emd_46799.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened masked map. dsDNA was masked to obtain higher resolution of the protein and bound ssDNA in the core of the complex. See related entries.
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: 0.876
Minimum - Maximum-3.0810716 - 4.8392696
Average (Standard dev.)-0.0007179957 (±0.10079428)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: Unsharpened masked map

Fileemd_46799_additional_1.map
AnnotationUnsharpened masked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_46799_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_46799_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: UvrD1
    • DNA: DNA strand
    • DNA: DNA

-
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

-
Macromolecule #1: UvrD1

MacromoleculeName: UvrD1 / type: protein_or_peptide / ID: 1 / Details: A dimer of UvrD1 is present in this sample. / 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

-
Macromolecule #2: DNA strand

MacromoleculeName: DNA strand / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
SequenceString:
GTTGGTCGGC AGCAGGGCTT TTTTTTTTTT TTTTTTTT

-
Macromolecule #3: DNA

MacromoleculeName: DNA / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
SequenceString:
GCCCTGCTGC CGACCAAC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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 / 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

+
Image processing

Particle selectionNumber selected: 634557
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 51008
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more