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- EMDB-77061: 95-bp double-stranded DNA minicircle: poly(A:T) model -

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Basic information

Entry
Database: EMDB / ID: EMD-77061
Title95-bp double-stranded DNA minicircle: poly(A:T) model
Map data
Sample
  • Complex: Synthetic 95-bp double-stranded DNA minicircle
    • Complex: DNA (95-MER)
      • DNA: DNA (95-MER)
    • Complex: DNA (95-MER)
      • DNA: DNA (95-MER)
KeywordsDNA minicircle / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.27 Å
AuthorsLiu Y / Qin PZ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145341 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131901 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127086 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Cryo-EM structure of a 95-base-pair double-stranded DNA minicircle at 5.3 Å resolution.
Authors: Yukang Liu / Kyu-Yeon Lee / Yao He / Donggyun Kim / Hongjian Chang / Vadim Cherezov / Juli Feigon / Peter Z Qin /
Abstract: Double-stranded DNA minicircles have been observed in a variety of biological settings and are also widely employed in biotechnology, therapeutic applications, and basic research. Here, we report a ...Double-stranded DNA minicircles have been observed in a variety of biological settings and are also widely employed in biotechnology, therapeutic applications, and basic research. Here, we report a cryo-EM structure of a 95-base-pair minicircle (dsMC95) at a 5.3 Å resolution. dsMC95 forms a closed ring as designed and no severe local duplex disruption is observed. The two DNA strands are fully resolved, with the major and minor grooves clearly distinguishable. Analysis reveals a nine-fold periodicity in the helical twist, which corresponds to approximately 10.56 base pairs per turn. Together with groove width analysis, the data indicate that dsMC95 maintains a B-DNA configuration. The dsMC95 ring exhibits modest in-plane ellipticity and small out-of-plane displacement, with outward-facing grooves widened and inward-facing ones compressed. The dsMC95 structure, which is the only free DNA cryo-EM structure with a resolution better than 6 Å to date, allows comparison to other structures to better understand DNA physical features such as bending. The findings advance our understanding of DNA structure under topological constraints and will inform studies of naturally occurring small circular DNA as well as the manipulation of DNA in nanotechnology applications.
History
DepositionMay 5, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77061.png

Downloads & links

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Map

FileDownload / File: emd_77061.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 512 pix.
= 261.12 Å		0.51 Å/pix.
x 512 pix.
= 261.12 Å		0.51 Å/pix.
x 512 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.0081340335 - 0.08121776
Average (Standard dev.)0.00005855407 (±0.0029396066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77061_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77061_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77061_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Synthetic 95-bp double-stranded DNA minicircle

EntireName: Synthetic 95-bp double-stranded DNA minicircle
Components
  • Complex: Synthetic 95-bp double-stranded DNA minicircle
    • Complex: DNA (95-MER)
      • DNA: DNA (95-MER)
    • Complex: DNA (95-MER)
      • DNA: DNA (95-MER)

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Supramolecule #1: Synthetic 95-bp double-stranded DNA minicircle

SupramoleculeName: Synthetic 95-bp double-stranded DNA minicircle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 29.4 KDa

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Supramolecule #2: DNA (95-MER)

SupramoleculeName: DNA (95-MER) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Supramolecule #3: DNA (95-MER)

SupramoleculeName: DNA (95-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: DNA (95-MER)

MacromoleculeName: DNA (95-MER) / type: dna / ID: 1
Details: The deposited coordinates represent a surrogate poly(dA) sequence instead of the actual DNA sequence
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 29.709711 KDa
SequenceString: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA) ...String:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)

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Macromolecule #2: DNA (95-MER)

MacromoleculeName: DNA (95-MER) / type: dna / ID: 2
Details: The deposited coordinates represent a surrogate poly(dT) sequence instead of the actual DNA sequence.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.853314 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(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

Concentration0.70 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMTris(hydroxymethyl)aminomethane hydrochloride
1.0 mMEthylenediaminetetraacetic acid disodium salt

Details: 20 mM Tris-HCl (pH 8.0) and 1 mM EDTA
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 30028 / Average exposure time: 3.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1412668
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 344629
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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