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- EMDB-65952: Cryo-EM structure of I3L-ssDNA double-ring complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65952
TitleCryo-EM structure of I3L-ssDNA double-ring complex
Map dataCryo-EM structure of I3L-ssDNA double-ring complex
Sample
  • Complex: I3L double-ring complex
    • Protein or peptide: Protein OPG079
KeywordsssDNA-binding / DNA replication / double-ring complex / OB-like / VIRAL PROTEIN
Function / homologyPoxvirus I3 ssDNA-binding / Poxvirus I3 ssDNA-binding protein / chromosome condensation / single-stranded DNA binding / host cell cytoplasm / Protein OPG079
Function and homology information
Biological speciesMonkeypox virus Zaire-96-I-16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMa J / Yang K
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cryo-EM structure of I3L-ssDNA double-ring complex
Authors: Ma J / Yang K
History
DepositionAug 23, 2025-
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_65952.png

Downloads & links

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Map

FileDownload / File: emd_65952.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of I3L-ssDNA double-ring complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.03709452 - 0.062493786
Average (Standard dev.)0.0002995291 (±0.0026439836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65952_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65952_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : I3L double-ring complex

EntireName: I3L double-ring complex
Components
  • Complex: I3L double-ring complex
    • Protein or peptide: Protein OPG079

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Supramolecule #1: I3L double-ring complex

SupramoleculeName: I3L double-ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Monkeypox virus Zaire-96-I-16

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Macromolecule #1: Protein OPG079

MacromoleculeName: Protein OPG079 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus Zaire-96-I-16
Molecular weightTheoretical: 25.412959 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHGSD SLQTCAGVIE YAKSISKSNA KCIEYVTLNA SQYANCSSIS IKLTDSLSSQ MTSTFIMLEG ETKLYKNKSK QDRSDGYFL KIKVTAASPM LYQLLEAVYG NITHKERIPN SLHSLSAETI TEKTFKDESI FINKLNGAMV EYVSTGESSI L RSIEGELE ...String:
MHHHHHHGSD SLQTCAGVIE YAKSISKSNA KCIEYVTLNA SQYANCSSIS IKLTDSLSSQ MTSTFIMLEG ETKLYKNKSK QDRSDGYFL KIKVTAASPM LYQLLEAVYG NITHKERIPN SLHSLSAETI TEKTFKDESI FINKLNGAMV EYVSTGESSI L RSIEGELE SLSKRERQLA KAIITPVVFY RSGTETKITF ALKKLIIDRE VVANVIGLSG DSERVSMTEN

UniProtKB: Protein OPG079

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D8 (2x8 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 340355
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9wgb:
Cryo-EM structure of I3L-ssDNA double-ring complex

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