9Q3G: Human AGO1

Cryo-EM structure of human AGO1 in complex with guide RNA. Determined by electron microscopy at 3.3 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Trichoplusia ni
Chains: 2
Atoms: 6,480
Mol. weight: 100.4 kDa
Released: 29 Oct 2025

Explore 9Q3G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3G contains 33 α-helices and 40 β-strands across 1 chain. 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: 33 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	34-40	7	1
β-strand	42-46	5	2
β-strand	51-56	6	3
β-strand	57-59	3	4
α-helix	66-79	14
α-helix	81-85	5
β-strand	91-92	2	3
β-strand	97-100	4	3
β-strand	128-130	3	4
β-strand	134-137	4	3
α-helix	138-147	10
α-helix	155-163	9
α-helix	166-171	6
β-strand	173-175	3	2
β-strand	178-181	4	2
β-strand	194-206	13	2
β-strand	211-223	13	2
α-helix	228-236	9
α-helix	250-259	10
α-helix	307-313	7
α-helix	323-325	3
α-helix	356-366	11
α-helix	370-384	15
α-helix	386-388	3
α-helix	390-395	6
β-strand	398-399	2	2
α-helix	403	1
β-strand	404-410	7	1
α-helix	411-413	3
β-strand	416-417	2	5
β-strand	419	1	6
β-strand	425-426	2	5
β-strand	432	1	7
β-strand	439	1	6
β-strand	442	1	8
β-strand	446	1	9
β-strand	450-453	4	10
α-helix	457-459	3
α-helix	462-479	18
β-strand	483	1	9
β-strand	490-492	3	10
α-helix	496-498	3
α-helix	499-509	11
β-strand	516-520	5	10
α-helix	526-533	8
α-helix	534-538	5
β-strand	542-546	5	10
α-helix	548-551	4
α-helix	555-569	15
β-strand	572	1	8
β-strand	575-576	2	5
α-helix	578-580	3
α-helix	584-586	3
β-strand	590-597	8	1
α-helix	599-600	2
β-strand	608-615	8	1
β-strand	623-630	8	1
α-helix	640-655	16
β-strand	661-666	6	1
α-helix	674-692	19
β-strand	699-706	8	1
β-strand	713-715	3	1
β-strand	722	1	11
β-strand	727	1	11
α-helix	728-729	2
β-strand	732-734	3	1
β-strand	745-749	5	1
β-strand	761-767	7	1
α-helix	774-784	11
β-strand	793	1	7
α-helix	799-814	16
α-helix	836-844	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-1	A	protein	871	Homo sapiens	Q9UL18 (AlphaFold model)
Non-homogenous guide RNA	B	RNA	8	Trichoplusia ni

Sequence of entity 1 (A), FASTA

>9Q3G_1 Protein argonaute-1 (chains A)
GAMGSMDYKDDDDKMEAGPSGAAAGAYLPPLQQVFQAPRRPGIGTVGKPIKLLANYFEVD
IPKIDVYHYEVDIKPDKCPRRVNREVVEYMVQHFKPQIFGDRKPVYDGKKNIYTVTALPI
GNERVDFEVTIPGEGKDRIFKVSIKWLAIVSWRMLHEALVSGQIPVPLESVQALDVAMRH
LASMRYTPVGRSFFSPPEGYYHPLGGGREVWFGFHQSVRPAMWKMMLNIDVSATAFYKAQ
PVIEFMCEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQMKRKYRVCNVTRRP
ASHQTFPLQLESGQTVECTVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVA
GQRCIKKLTDNQTSTMIKATARSAPDRQEEISRLMKNASYNLDPYIQEFGIKVKDDMTEV
TGRVLPAPILQYGGRNRAIATPNQGVWDMRGKQFYNGIEIKVWAIACFAPQKQCREEVLK
NFTDQLRKISKDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYSGLQLIIVILPGKTPV
YAEVKRVGDTLLGMATQCVQVKNVVKTSPQTLSNLCLKINVKLGGINNILVPHQRSAVFQ
QPVIFLGADVTHPPAGDGKKPSITAVVGSMDAHPSRYCATVRVQRPRQEIIEDLSYMVRE
LLIQFYKSTRFKPTRIIFYRDGVPEGQLPQILHYELLAIRDACIKLEKDYQPGITYIVVQ
KRHHTRLFCADKNERIGKSGNIPAGTTVDTNITHPFEFDFYLCSHAGIQGTSRPSHYYVL
WDDNRFTADELQILTYQLCHTYVRCTRSVSIPAPAYYARLVAFRARYHLVDKEHDSGEGS
HISGQSNGRDPQALAKAVQVHQDTLRTMYFA

Sequence of entity 2 (B), FASTA

>9Q3G_2 Non-homogenous guide RNA (chains B)
NNNNNNNN

Primary citation

Neurodevelopmental disorder-linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3'→5' trimming. Savidge, A., Zhang, H., Annasaheb Adhav, V. et al. Proc Natl Acad Sci U S A (2025) 122:e2524644122-e2524644122. DOI 10.1073/pnas.2524644122 · PubMed

Other PDB entries of the same protein (UniProt Q9UL18 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KRE 1.75 Å, Structure of Human Argonaute-1 bound to endogenous Sf9 RNA
4KRF 2.1 Å, Structure of Human Argonaute-1 let-7 complex
4KXT 2.29 Å, Structure of human ARGONAUTE1 in complex with guide RNA
1SI2 2.6 Å, Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like…
1SI3 2.6 Å, Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like…
5W6V 2.83 Å, The Structure of human Argonaute-1 in complex with the hook motif of human GW182
9Q3F 3.3 Å, Structure of neurodevelopmental mutant AGO1 F180del in complex with guide RNA

Browse structure collections

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