9W5I: AGO maturation complex (AMC): AGO2-miRNA duplex

Name: PDB 9W5I: AGO maturation complex (AMC): AGO2-miRNA duplex in complex with Hsp90 beta and co-chaperone p23
Published: 2026-04-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

AGO maturation complex (AMC): AGO2-miRNA duplex in complex with Hsp90 beta and co-chaperone p23. Determined by electron microscopy at 2.63 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 2.63 Å
Organism: Homo sapiens
Chains: 6
Atoms: 18,185
Mol. weight: 297.88 kDa
Ligands: MG, ATP
Released: 22 Apr 2026

Explore 9W5I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W5I contains 88 α-helices and 115 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 30 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	1
β-strand	18-19	2	2
α-helix	21-30	10
α-helix	36-38	3
α-helix	39-57	19
α-helix	62-65	4
β-strand	73-78	6	3
β-strand	83-88	6	3
α-helix	95-97	3
α-helix	98-102	5
β-strand	104-105	2	4
α-helix	109-116	8
α-helix	132-138	7
β-strand	140-148	9	3
β-strand	154-159	6	3
β-strand	164-169	6	3
β-strand	178-185	8	3
α-helix	191-193	3
α-helix	195-205	11
β-strand	213-218	6	3
β-strand	277-281	5	3
α-helix	288-290	3
α-helix	298-309	12
β-strand	315-323	9	5
β-strand	329-336	8	5
β-strand	353-357	5	5
β-strand	360-364	5	5
α-helix	372-374	3
β-strand	378-383	6	5
β-strand	388	1	6
β-strand	395	1	6
α-helix	399-419	21
α-helix	423-432	10
α-helix	434-443	10
α-helix	448-451	4
α-helix	452-454	3
β-strand	456-457	2	7
β-strand	458-459	2	8
β-strand	467-468	2	7
α-helix	469-475	7
β-strand	482-487	6	8
α-helix	491-495	5
α-helix	501-505	5
β-strand	510-513	4	8
α-helix	516-524	9
β-strand	527-528	2	8
β-strand	531-535	5	8
α-helix	547-559	13
α-helix	561-570	10
β-strand	578-580	3	9
β-strand	589-592	4	9
β-strand	598	1	10
α-helix	600-607	8
α-helix	616-618	3
β-strand	621	1	10
α-helix	623-624	2
β-strand	625-628	4	9
α-helix	633-644	12
α-helix	649-665	17
α-helix	673-688	16

Chain B: 28 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	3
β-strand	18-19	2	4
α-helix	21-30	10
α-helix	38-58	21
α-helix	62-65	4
β-strand	73-78	6	1
β-strand	83-88	6	1
α-helix	95-100	6
β-strand	104-105	2	2
α-helix	109-116	8
α-helix	132-138	7
β-strand	140-148	9	1
β-strand	155-159	5	1
β-strand	164-169	6	1
β-strand	178-185	8	1
α-helix	190-193	4
α-helix	195-205	11
β-strand	213-215	3	1
β-strand	216-218	3	11
β-strand	277-279	3	11
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
β-strand	315-323	9	12
β-strand	329-336	8	12
β-strand	353-357	5	12
β-strand	360-364	5	12
α-helix	372-374	3
β-strand	378-383	6	12
β-strand	388	1	13
β-strand	395	1	13
α-helix	400-419	20
α-helix	425-432	8
α-helix	435-443	9
α-helix	446-448	3
α-helix	449-452	4
β-strand	456-457	2	14
β-strand	458-459	2	15
β-strand	467-468	2	14
α-helix	469-475	7
β-strand	483-487	5	15
α-helix	491-495	5
α-helix	498-500	3
α-helix	501-506	6
β-strand	511-513	3	15
α-helix	517-522	6
β-strand	528	1	16
β-strand	531	1	16
β-strand	533-535	3	15
β-strand	538	1	17
α-helix	547-559	13
α-helix	561-570	10
β-strand	577-580	4	18
β-strand	589-592	4	18
β-strand	593	1	17
α-helix	600-607	8
β-strand	625-628	4	18
α-helix	633-644	12
α-helix	649-665	17
α-helix	673-688	16

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	19
α-helix	3-5	3
β-strand	6-10	5	20
β-strand	14-19	6	20
β-strand	25-31	7	19
β-strand	36-42	7	19
β-strand	47-53	7	19
β-strand	55	1	21
β-strand	59-68	10	20
β-strand	73-79	7	20
β-strand	90	1	21
β-strand	99-101	3	20
α-helix	117-128	12

Chain D: 28 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	53-58	6	22
β-strand	59-62	4	23
α-helix	68-81	14
α-helix	91-92	2
β-strand	93-94	2	22
β-strand	99-102	4	22
β-strand	113	1	23
β-strand	116	1	23
β-strand	129-132	4	23
β-strand	136-139	4	22
α-helix	140-149	10
β-strand	167	1	22
α-helix	202-204	3
β-strand	209	1	24
α-helix	230-238	9
α-helix	243-247	5
α-helix	249-251	3
α-helix	252-261	10
β-strand	266-267	2	25
β-strand	272	1	26
β-strand	275	1	26
β-strand	279-280	2	25
β-strand	281-288	8	27
β-strand	294-297	4	28
β-strand	303-306	4	28
α-helix	308-314	7
β-strand	326-330	5	27
β-strand	339	1	27
α-helix	412-417	6
β-strand	418-419	2	29
β-strand	427-428	2	29
β-strand	431	1	30
β-strand	434	1	30
β-strand	444	1	31
β-strand	448	1	32
β-strand	451-455	5	33
α-helix	464-480	17
β-strand	485	1	32
β-strand	492-494	3	33
α-helix	498-500	3
α-helix	501-511	11
β-strand	517-522	6	33
α-helix	528-534	7
α-helix	535-540	6
β-strand	544-548	5	33
α-helix	550-553	4
α-helix	557-571	15
β-strand	574	1	31
β-strand	577-578	2	29
α-helix	580-582	3
α-helix	585-588	4
β-strand	591-599	9	34
α-helix	609	1
β-strand	610-617	8	34
β-strand	625-632	8	34
α-helix	642-657	16
β-strand	663-669	7	34
α-helix	673-675	3
α-helix	676-694	19
β-strand	699	1	24
β-strand	701-707	7	34
α-helix	730-731	2
β-strand	750	1	35
β-strand	765	1	35
β-strand	766-770	5	34
α-helix	776-787	12
β-strand	795	1	30
α-helix	801-816	16
α-helix	838-844	7
α-helix	850-854	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-beta	A, B	protein	724	Homo sapiens	P08238 (AlphaFold model)
Prostaglandin E synthase 3	C	protein	160	Homo sapiens	Q15185 (AlphaFold model)
Protein argonaute-2	D	protein	859	Homo sapiens	Q9UKV8 (AlphaFold model)
RNA (5'-r(pupgpapgpgpupapgpupapgpgpupupgpupapupapgpupu)-3')	E	RNA	22	Homo sapiens
RNA (5'-r(pcpupapupapcpapapupcpupapcpupgpupcpupupupcpu)-3')	F	RNA	22	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>9W5I_1 Heat shock protein HSP 90-beta (chains A, B)
MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLT
DPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAG
ADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTK
VILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEE
DKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEE
YGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRV
FIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELA
EDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQ
KSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEG
LELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTA
NMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFE
TALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRM
EEVD

Sequence of entity 2 (C), FASTA

>9W5I_2 Prostaglandin E synthase 3 (chains C)
MQPASAKWYDRRDYVFIEFCVEDSKDVNVNFEKSKLTFSCLGGSDNFKHLNEIDLFHCID
PNDSKHKRTDRSILCCLRKGESGQSWPRLTKERAKLNWLSVDFNNWKDWEDDSDEDMSNF
DRFSEMMNNMGGDEDVDLPEVDGADDDSQDSDDEKMPDLE

Sequence of entity 3 (D), FASTA

>9W5I_3 Protein argonaute-2 (chains D)
MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELD
IKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLP
GEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRS
FFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDF
KSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQES
GQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQ
TSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILY
GGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRD
AGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVL
GMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTH
PPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFK
PTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDK
NERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQ
ILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQ
ALAKAVQVHQDTLRTMYFA

Sequence of entity 4 (E), FASTA

>9W5I_4 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') (chains E)
UGAGGUAGUAGGUUGUAUAGUU

Sequence of entity 5 (F), FASTA

>9W5I_5 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') (chains F)
CUAUACAAUCUACUGUCUUUCU

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Structural basis for chaperone-guided assembly of RNA-induced silencing complex. Lee, Y.Y., Jeong, M., Lee, H. et al. Nature (2026) 655:1339-1348. DOI 10.1038/s41586-026-10640-2 · PubMed

Other PDB entries of the same protein (UniProt P08238 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9D9I 1.5 Å, Human Hsp90b nucleotide binding domain in complex with BRI2312
6N8Y 1.55 Å, Hsp90-beta bound to PU-11-trans
5UCJ 1.69 Å, Hsp90b N-terminal domain with inhibitors
7ULJ 1.82 Å, Hsp90b N-terminal domain in complex with 42C
9D9H 1.96 Å, Human Hsp90b nucleotide binding domain in complex with BRI2311
5UC4 2.05 Å, Hsp90b N-terminal domain with inhibitors
3FWV 2.2 Å, Crystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Complex with MEEVF Peptide
3NMQ 2.2 Å, Hsp90b N-terminal domain in complex with EC44, a pyrrolo-pyrimidine methoxypyridine…
3PRY 2.28 Å, Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution
1UYM 2.45 Å, Human Hsp90-beta with PU3 (9-Butyl-8(3,4,5-trimethoxy-benzyl)-9H-purin-6-ylamine)
3UQ3 2.6 Å, TPR2AB-domain:pHSP90-complex of yeast Sti1
5UCH 2.65 Å, Hsp90b N-terminal domain with inhibitors

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