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- EMDB-71404: DnaB complex binding with ssDNA and dTDP-AlFx -

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Basic information

Entry
Database: EMDB / ID: EMD-71404
TitleDnaB complex binding with ssDNA and dTDP-AlFx
Map data
Sample
  • Complex: Ternary complex of DnaB with ssDNA and dTDP
    • Protein or peptide: Replicative DNA helicase DnaB
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION
KeywordsHelicase / DNA BINDING PROTEIN
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA 5'-3' helicase / 5'-3' DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLiu C / Eliason WK / Berger JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2026
Title: Cellular replisomes are powered by flex-fuel motors for unwinding DNA.
Authors: Fahad Rashid / Sushil Pangeni / Chuan Liu / Harish Kumar / Gyeongtae Sun Moon / Qianyun Yan / Taekjip Ha / James M Berger /
Abstract: DNA replication relies on hexameric, ring-shaped helicases to unwind parental DNA for supporting fork progression over tens of thousands of base pairs. Oddly, biochemical studies have suggested that, ...DNA replication relies on hexameric, ring-shaped helicases to unwind parental DNA for supporting fork progression over tens of thousands of base pairs. Oddly, biochemical studies have suggested that, on their own, replicative helicases are rather limited motors that struggle to couple rapid movement to nucleotide turnover (typically believed to be solely ATP). Here, single-molecule studies reveal that when properly loaded, the Escherichia coli (E. coli) replicative helicase, DnaB, is a tremendously fast single-stranded DNA translocase that moves up to three times more rapidly than the replisome (3 knt/s). Translocation is highly processive, resistant to pulling force/high salt, and can displace short, 3'-tailed DNA duplexes without apparent changes in speed. Surprisingly, we find that the loader for DnaB, DnaC, can use any rNTP or dATP for depositing DnaB onto ssDNA and that the helicase itself also must hydrolyze nucleotide for stable loading. DnaB translocation also turns out to be supported by any r/dNTP, a property shown to extend to the eukaryotic CMG replicative helicase. Overall, the DNA unwinding engines that support cellular replisomes are highly indiscriminate of their fuel source, a feature that may be of utility during times when cells encounter nucleotide pool stress but have committed to DNA synthesis.
History
DepositionJun 24, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71404.png

Downloads & links

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Map

FileDownload / File: emd_71404.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 360 pix.
= 349.2 Å		0.97 Å/pix.
x 360 pix.
= 349.2 Å		0.97 Å/pix.
x 360 pix.
= 349.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.153
Minimum - Maximum-0.7995217 - 1.2145317
Average (Standard dev.)-0.0000058734845 (±0.023061145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 349.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EMReady postprocessed map

Fileemd_71404_additional_1.map
AnnotationEMReady postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71404_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71404_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of DnaB with ssDNA and dTDP

EntireName: Ternary complex of DnaB with ssDNA and dTDP
Components
  • Complex: Ternary complex of DnaB with ssDNA and dTDP
    • Protein or peptide: Replicative DNA helicase DnaB
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-DIPHOSPHATE
  • Ligand: TETRAFLUOROALUMINATE ION

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Supramolecule #1: Ternary complex of DnaB with ssDNA and dTDP

SupramoleculeName: Ternary complex of DnaB with ssDNA and dTDP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)

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Macromolecule #1: Replicative DNA helicase DnaB

MacromoleculeName: Replicative DNA helicase DnaB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA 5'-3' helicase
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 50.699445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSELFSERIP PQSIEAEQAV LGAVFLDPAA LVPASEILIP EDFYRAAHQK IFHAMLRVAD RGEPVDLVTV TAELAASEQL EEIGGVSYL SELADAVPTA ANVEYYARIV EEKSVLRRLI RTATSIAQDG YTREDEIDVL LDEADRKIME VSQRKHSGAF K NIKDILVQ ...String:
MSELFSERIP PQSIEAEQAV LGAVFLDPAA LVPASEILIP EDFYRAAHQK IFHAMLRVAD RGEPVDLVTV TAELAASEQL EEIGGVSYL SELADAVPTA ANVEYYARIV EEKSVLRRLI RTATSIAQDG YTREDEIDVL LDEADRKIME VSQRKHSGAF K NIKDILVQ TYDNIEMLHN RDGEITGIPT GFTELDRMTS GFQRSDLIIV AARPSVGKTA FALNIAQNVA TKTNENVAIF SL EMSAQQL VMRMLCAEGN INAQNLRTGK LTPEDWGKLT MAMGSLSNAG IYIDDTPSIR VSDIRAKCRR LKQESGLGMI VID YLQLIQ GSGRSKENRQ QEVSEISRSL KALARELEVP VIALSQLSRS VEQRQDKRPM MSDIRESGSI EQDADIVAFL YRDD YYNKD SENKNIIEII IAKQRNGPVG TVQLAFIKEY NKFVNLERRF DEAQIPPGA

UniProtKB: Replicative DNA helicase DnaB

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Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.909549 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: THYMIDINE-5'-DIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: TYD
Molecular weightTheoretical: 402.188 Da
Chemical component information

ChemComp-TYD:
THYMIDINE-5'-DIPHOSPHATE

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Macromolecule #5: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 154856
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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