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- PDB-9w5i: AGO maturation complex (AMC): AGO2-miRNA duplex in complex with H... -

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Entry
Database: PDB / ID: 9w5i
TitleAGO maturation complex (AMC): AGO2-miRNA duplex in complex with Hsp90 beta and co-chaperone p23
Components
  • Heat shock protein HSP 90-beta
  • Prostaglandin E synthase 3
  • Protein argonaute-2
  • RNA (5'-R(P*CP*UP*AP*UP*AP*CP*AP*AP*UP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*UP*CP*U)-3')
  • RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')
KeywordsCHAPERONE / Hsp90 / p23 / Argonaute / miRNA / AGO2 / co-chaperone
Function / homology
Function and homology information


prostaglandin-E synthase / prostaglandin-E synthase activity / HSP90-CDC37 chaperone complex / : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs ...prostaglandin-E synthase / prostaglandin-E synthase activity / HSP90-CDC37 chaperone complex / : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / Regulation of PTEN mRNA translation / miRNA-mediated gene silencing by mRNA destabilization / negative regulation of amyloid precursor protein biosynthetic process / RNA stabilization / telomerase activity / aryl hydrocarbon receptor complex / Small interfering RNA (siRNA) biogenesis / prostanoid biosynthetic process / Regulation of CDH1 mRNA translation by microRNAs / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / histone methyltransferase binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / dynein axonemal particle / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / receptor ligand inhibitor activity / miRNA processing / RNA 7-methylguanosine cap binding / pre-miRNA processing / protein kinase regulator activity / regulation of synapse maturation / positive regulation of protein localization to cell surface / prostaglandin biosynthetic process / siRNA binding / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / siRNA processing / ATP-dependent protein binding / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / TGFBR3 expression / regulatory ncRNA-mediated gene silencing / telomerase holoenzyme complex / Regulation of RUNX1 Expression and Activity / P-body assembly / miRNA binding / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / protein phosphatase activator activity / HSF1-dependent transactivation / protein folding chaperone complex / response to unfolded protein / Regulation of MECP2 expression and activity / Attenuation phase / HSF1 activation / chaperone-mediated protein complex assembly / axonal growth cone / RHOBTB2 GTPase cycle / telomere maintenance via telomerase / core promoter sequence-specific DNA binding / Purinergic signaling in leishmaniasis infection / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of telomere maintenance via telomerase / supramolecular fiber organization / heat shock protein binding / peptide binding / Nuclear events stimulated by ALK signaling in cancer / DNA polymerase binding / RNA endonuclease activity / translation initiation factor activity / protein folding chaperone / cellular response to interleukin-4 / ESR-mediated signaling / negative regulation of translational initiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / placenta development / telomere maintenance / nitric-oxide synthase regulator activity / post-embryonic development
Similarity search - Function
Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / Protein argonaute-2 / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain ...Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / Protein argonaute-2 / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / HSP20-like chaperone / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Heat shock protein HSP 90-beta / Prostaglandin E synthase 3 / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsLee, H. / Jeong, M.-S. / Lee, Y.-Y. / Lee, J.-H. / Lee, D. / Kim, V.N. / Roh, S.-H.
Funding support Korea, Republic Of, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-beta
B: Heat shock protein HSP 90-beta
C: Prostaglandin E synthase 3
D: Protein argonaute-2
E: RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')
F: RNA (5'-R(P*CP*UP*AP*UP*AP*CP*AP*AP*UP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,88411
Polymers296,7966
Non-polymers1,0875
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 4 molecules ABCD

#1: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP 84 / HSP84 / Heat shock protein family C member 3


Mass: 83384.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPC3, HSPCB / Production host: Homo sapiens (human) / References: UniProt: P08238
#2: Protein Prostaglandin E synthase 3 / Cytosolic prostaglandin E2 synthase / cPGES / Hsp90 co-chaperone / Progesterone receptor complex ...Cytosolic prostaglandin E2 synthase / cPGES / Hsp90 co-chaperone / Progesterone receptor complex p23 / Telomerase-binding protein p23


Mass: 18720.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGES3, P23, TEBP / Production host: Homo sapiens (human) / References: UniProt: Q15185, prostaglandin-E synthase
#3: Protein Protein argonaute-2 / Argonaute2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation ...Argonaute2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF-2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 97350.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Homo sapiens (human)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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RNA chain , 2 types, 2 molecules EF

#4: RNA chain RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')


Mass: 7118.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human let-7a-1 5p strand / Source: (synth.) Homo sapiens (human)
#5: RNA chain RNA (5'-R(P*CP*UP*AP*UP*AP*CP*AP*AP*UP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*UP*CP*U)-3')


Mass: 6839.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human let-7a-1 3p strand / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 5 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of AGO2 with miRNA and Hsp90-p23 / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 69.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1225410 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 111.1 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002918624
ELECTRON MICROSCOPYf_angle_d0.521625321
ELECTRON MICROSCOPYf_chiral_restr0.03962830
ELECTRON MICROSCOPYf_plane_restr0.00333086
ELECTRON MICROSCOPYf_dihedral_angle_d11.90893006

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