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- EMDB-61765: Cryo-EM Structure of EfPiwi-piRNA-target (25-nt) in the presence ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61765
TitleCryo-EM Structure of EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K32A/K35A
Map data
Sample
  • Complex: EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K32A/K35A
KeywordsPiwi protein / Pi-RNA / Argonaute / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex / RNA BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi ZQ / Xu QK / Wu JP / Shen EZ
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM Structure of EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K32A/K35A
Authors: Li ZQ / Xu QK / Wu JP / Shen EZ
History
DepositionSep 29, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61765.png

Downloads & links

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Map

FileDownload / File: emd_61765.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 192 pix.
= 176.64 Å		0.92 Å/pix.
x 192 pix.
= 176.64 Å		0.92 Å/pix.
x 192 pix.
= 176.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.39549544 - 0.67338955
Average (Standard dev.)0.00002570443 (±0.017737329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 176.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61765_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_61765_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 : EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K...

EntireName: EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K32A/K35A
Components
  • Complex: EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K32A/K35A

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Supramolecule #1: EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K...

SupramoleculeName: EfPiwi-piRNA-target (25-nt) in the presence of EmGTSF1Q22A/R25A/K32A/K35A
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: FEI FALCON IV (4k 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: 2.0 µm / Nominal defocus min: 1.5 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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173340
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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