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

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Basic information

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 / Regulation of PTEN mRNA translation / miRNA-mediated gene silencing by mRNA destabilization / negative regulation of proteasomal protein catabolic process / negative regulation of amyloid precursor protein biosynthetic process / Aryl hydrocarbon receptor signalling / telomerase activity / RNA stabilization / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Regulation of CDH1 mRNA translation by microRNAs / aryl hydrocarbon receptor complex / prostanoid biosynthetic process / 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 / receptor ligand inhibitor activity / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / RNA 7-methylguanosine cap binding / pre-miRNA processing / regulation of synapse maturation / siRNA processing / protein kinase regulator activity / siRNA binding / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of protein localization to cell surface / prostaglandin biosynthetic process / ATP-dependent protein binding / RISC complex / TGFBR3 expression / telomerase holoenzyme complex / regulatory ncRNA-mediated gene silencing / 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / RNA polymerase II complex binding / Sema3A PAK dependent Axon repulsion / protein phosphatase activator activity / The NLRP3 inflammasome / regulation of protein ubiquitination / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / protein folding chaperone complex / response to unfolded protein / Attenuation phase / HSF1 activation / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / axonal growth cone / 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 / Nuclear events stimulated by ALK signaling in cancer / positive regulation of telomere maintenance via telomerase / supramolecular fiber organization / heat shock protein binding / DNA polymerase binding / peptide binding / RNA endonuclease activity / translation initiation factor activity / protein folding chaperone / negative regulation of translational initiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / ESR-mediated signaling / cellular response to interleukin-4 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / telomere maintenance / placenta development / 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: 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, V.N. / Roh, S.-H.
History
DepositionAug 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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