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- EMDB-65662: Consensus map of Hsp90-p23-AGO2-miRNA duplex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-65662
TitleConsensus map of Hsp90-p23-AGO2-miRNA duplex
Map data
Sample
  • Complex: Complex of AGO2 with miRNA and Hsp90-p23
KeywordsHsp90 / p23 / Argonaute / miRNA / AGO2 / chaperone / co-chaperone
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsLee H / Jeong M-S / Lee Y-Y / Lee J-H / Lee D / Kim VN / Roh S-H
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structural basis for chaperone-guided RISC assembly
Authors: Jeong M-S / Lee Y-Y / Lee H / Lee J-H / Lee D / Kim VN / Roh S-H
History
DepositionAug 1, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65662.png

Downloads & links

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Map

FileDownload / File: emd_65662.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 280 pix.
= 318.72 Å		1.14 Å/pix.
x 280 pix.
= 318.72 Å		1.14 Å/pix.
x 280 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0429
Minimum - Maximum-0.40516993 - 1.4769849
Average (Standard dev.)-0.00018206115 (±0.01634568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 318.71997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65662_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65662_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_65662_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 : Complex of AGO2 with miRNA and Hsp90-p23

EntireName: Complex of AGO2 with miRNA and Hsp90-p23
Components
  • Complex: Complex of AGO2 with miRNA and Hsp90-p23

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Supramolecule #1: Complex of AGO2 with miRNA and Hsp90-p23

SupramoleculeName: Complex of AGO2 with miRNA and Hsp90-p23 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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

BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1225410
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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