9Q3F: Neurodevelopmental mutant AGO1 F180del

Structure of neurodevelopmental mutant AGO1 F180del in complex with guide RNA. Determined by electron microscopy at 3.3 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Trichoplusia ni
Chains: 2
Atoms: 6,615
Mol. weight: 101.32 kDa
Released: 5 Nov 2025

Explore 9Q3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3F contains 29 α-helices and 52 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: 29 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	1
β-strand	38-40	3	2
β-strand	42-46	5	3
β-strand	51-52	2	4
β-strand	53-56	4	5
α-helix	66-79	14
α-helix	81-84	4
β-strand	91-92	2	5
β-strand	97-100	4	5
β-strand	112-113	2	6
β-strand	128-129	2	6
β-strand	136-137	2	4
α-helix	139-146	8
α-helix	151-152	2
α-helix	154-163	10
α-helix	166-171	6
β-strand	175	1	3
β-strand	178	1	3
β-strand	188	1	3
β-strand	194-202	9	3
β-strand	205	1	3
β-strand	210-221	12	3
α-helix	227-235	9
α-helix	252-259	8
β-strand	264	1	7
β-strand	280-281	2	8
α-helix	305-313	9
β-strand	324-327	4	8
β-strand	334-337	4	8
β-strand	343	1	7
β-strand	348	1	3
α-helix	355-365	11
α-helix	369-383	15
α-helix	385-387	3
α-helix	389-394	6
β-strand	397-398	2	3
α-helix	402	1
β-strand	403-405	3	2
β-strand	408-409	2	1
α-helix	410-412	3
β-strand	415-416	2	9
β-strand	418	1	10
β-strand	425	1	9
β-strand	428	1	11
β-strand	431	1	11
β-strand	438	1	10
β-strand	441	1	12
β-strand	449-451	3	13
α-helix	462-477	16
β-strand	489-490	2	13
α-helix	499-508	10
β-strand	515-519	5	13
α-helix	525-531	7
α-helix	532-536	5
β-strand	541-545	5	13
α-helix	547-550	4
α-helix	554-568	15
β-strand	571	1	12
β-strand	574-575	2	9
α-helix	582-585	4
β-strand	588-596	9	14
α-helix	605-606	2
β-strand	607-614	8	14
β-strand	622-624	3	14
β-strand	627-629	3	14
α-helix	639-654	16
β-strand	660-666	7	14
α-helix	673-691	19
β-strand	698-705	8	14
β-strand	712-714	3	2
β-strand	721	1	15
β-strand	726	1	15
β-strand	731-732	2	1
β-strand	744-747	4	14
β-strand	748	1	1
β-strand	760-766	7	14
α-helix	773-783	11
β-strand	792	1	11
α-helix	798-814	17
α-helix	836-843	8
α-helix	847-849	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-1	A	protein	870	Homo sapiens	Q9UL18 (AlphaFold model)
Non-homogenous guide RNA	B	RNA	8	Trichoplusia ni

Sequence of entity 1 (A), FASTA

>9Q3F_1 Protein argonaute-1 (chains A)
GAMGSMDYKDDDDKMEAGPSGAAAGAYLPPLQQVFQAPRRPGIGTVGKPIKLLANYFEVD
IPKIDVYHYEVDIKPDKCPRRVNREVVEYMVQHFKPQIFGDRKPVYDGKKNIYTVTALPI
GNERVDFEVTIPGEGKDRIFKVSIKWLAIVSWRMLHEALVSGQIPVPLESVQALDVAMRH
LASMRYTPVGRSFSPPEGYYHPLGGGREVWFGFHQSVRPAMWKMMLNIDVSATAFYKAQP
VIEFMCEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQMKRKYRVCNVTRRPA
SHQTFPLQLESGQTVECTVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVAG
QRCIKKLTDNQTSTMIKATARSAPDRQEEISRLMKNASYNLDPYIQEFGIKVKDDMTEVT
GRVLPAPILQYGGRNRAIATPNQGVWDMRGKQFYNGIEIKVWAIACFAPQKQCREEVLKN
FTDQLRKISKDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYSGLQLIIVILPGKTPVY
AEVKRVGDTLLGMATQCVQVKNVVKTSPQTLSNLCLKINVKLGGINNILVPHQRSAVFQQ
PVIFLGADVTHPPAGDGKKPSITAVVGSMDAHPSRYCATVRVQRPRQEIIEDLSYMVREL
LIQFYKSTRFKPTRIIFYRDGVPEGQLPQILHYELLAIRDACIKLEKDYQPGITYIVVQK
RHHTRLFCADKNERIGKSGNIPAGTTVDTNITHPFEFDFYLCSHAGIQGTSRPSHYYVLW
DDNRFTADELQILTYQLCHTYVRCTRSVSIPAPAYYARLVAFRARYHLVDKEHDSGEGSH
ISGQSNGRDPQALAKAVQVHQDTLRTMYFA

Sequence of entity 2 (B), FASTA

>9Q3F_2 Non-homogenous guide RNA (chains B)
AAAAAAAA

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
9Q3G 3.3 Å, Cryo-EM structure of human AGO1 in complex with guide RNA

Browse structure collections

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