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- EMDB-65659: Focused map of Hsp90-p23 and lumen from Hsp90-p23-AGO2-miRNA duplex -

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Basic information

Entry
Database: EMDB / ID: EMD-65659
TitleFocused map of Hsp90-p23 and lumen from 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: 3.04 Å
AuthorsLee H / Jeong M-S / Lee Y-Y / Lee J-H / Lee D / Kim VC / Roh S-H
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nature / Year: 2026
Title: Structural basis for chaperone-guided assembly of RNA-induced silencing complex.
Authors: Young-Yoon Lee / Minseok Jeong / Hansol Lee / Daniel Lee / Jaehyun Lee / Junsun Park / V Narry Kim / Soung-Hun Roh /
Abstract: The RNA-induced silencing complex (RISC), comprising an Argonaute (AGO) protein and a small RNA, is the central effector in RNA silencing. Small RNAs are loaded onto AGO as bulky duplexes in an HSP70- ...The RNA-induced silencing complex (RISC), comprising an Argonaute (AGO) protein and a small RNA, is the central effector in RNA silencing. Small RNAs are loaded onto AGO as bulky duplexes in an HSP70- and HSP90-dependent process, but the molecular mechanism remains poorly understood. Here we identify the human AGO-HSP90-p23 complex, which captures AGO in an RNA-free state, termed the AGO maturation complex (AMC). The purified AMC enables RNA loading and AGO folding, faithfully recapitulating de novo RISC assembly. Using cryogenic electron microscopy, we determined the structure of AMC bound to a microRNA duplex. In contrast to its conformation in the RISC, AGO adopts a highly open conformation in the AMC: the N domain and the RNA-binding module (PAZ-MID-PIWI) are fully detached and anchored to opposite sides of the HSP90 dimer, connected solely by the unfolded L1 linker. This arrangement exposes a positively charged cleft that accommodates an RNA duplex. AGO folding is facilitated by a small RNA duplex containing a 5'-terminal phosphate-but not by single-stranded RNAs-revealing a role for the RNA duplex as a chaperone-like cofactor that directs AGO domain assembly. These findings elucidate the RISC assembly mechanism and establish the AMC as a molecular tool for probing optimal RNA features and chemical modifications for the rational design of small interfering RNA therapeutics. Our study also sheds light on how chaperones, together with ligands, can guide the folding of client proteins.
History
DepositionAug 1, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65659.png

Downloads & links

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Map

FileDownload / File: emd_65659.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.104
Minimum - Maximum-0.304755 - 1.0219434
Average (Standard dev.)-0.00021161363 (±0.015082922)
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_65659_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_65659_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65659_half_map_2.map
Projections & Slices
AxesZYX

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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: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 206969
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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