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- EMDB-68835: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-... -

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Basic information

Entry
Database: EMDB / ID: EMD-68835
TitleCryo-EM structure of a triangular-prism protein-DNA complex (D17-11-2t-10a/10b-T)
Map dataD17-11-2t-10a/10b-T Trigonal prisms
Sample
  • Complex: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-11-2t-10a/10b-T)
KeywordsCryo-EM / bivalent aptamers / human alpha-thrombin / protein / DNA / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.61 Å
AuthorsNan XY
Funding support1 items
OrganizationGrant numberCountry
Other government22277017
CitationJournal: To Be Published
Title: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-11-2t-10a/10b-T)
Authors: Nan XY
History
DepositionJan 30, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68835.png

Downloads & links

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Map

FileDownload / File: emd_68835.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationD17-11-2t-10a/10b-T Trigonal prisms
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 460 pix.
= 446.2 Å		0.97 Å/pix.
x 460 pix.
= 446.2 Å		0.97 Å/pix.
x 460 pix.
= 446.2 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: 0.0692
Minimum - Maximum-0.08537668 - 0.49457306
Average (Standard dev.)-0.00006377535 (±0.015402681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 446.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: D17-11-2t-10a/10b-T Trigonal prisms

Fileemd_68835_half_map_1.map
AnnotationD17-11-2t-10a/10b-T Trigonal prisms
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: D17-11-2t-10a/10b-T Trigonal prisms

Fileemd_68835_half_map_2.map
AnnotationD17-11-2t-10a/10b-T Trigonal prisms
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of a triangular-prism protein-DNA complex (D17-...

EntireName: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-11-2t-10a/10b-T)
Components
  • Complex: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-11-2t-10a/10b-T)

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Supramolecule #1: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-...

SupramoleculeName: Cryo-EM structure of a triangular-prism protein-DNA complex (D17-11-2t-10a/10b-T)
type: complex / ID: 1 / Parent: 0
Details: Cryo-EM structure of a triangular-prism protein-DNA complex assembled by human alpha-thrombin and bivalent RE31-HD22 aptamers D17-11-2t-10a and D17-11-2t-10b
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.72 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 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 real images: 2674 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 50588
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 3857
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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