9OBD: Human Argonaute2

Crystal structure of human Argonaute2 in complex with a fully modified siRNA with a 5'-phenylpropargyl phosphate. Determined by X-ray diffraction at 2.02 Å resolution. Released 29 Apr 2026.

Method: X-ray diffraction
Resolution: 2.02 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 7,120
Mol. weight: 104.99 kDa
Ligands: MG, IPH, IPA
Released: 29 Apr 2026

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

Secondary structure: helices and β-sheets

9OBD contains 40 α-helices and 51 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: 40 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	27	1	1
α-helix	28	1
β-strand	36-42	7	2
β-strand	44-48	5	3
β-strand	53-62	10	4
α-helix	68-81	14
α-helix	83-87	5
β-strand	93-94	2	4
β-strand	99-102	4	4
β-strand	112-118	7	4
β-strand	127-139	13	4
α-helix	140-147	8
α-helix	156-173	18
β-strand	175-177	3	3
β-strand	180-183	4	3
β-strand	191-193	3	3
β-strand	196-208	13	3
β-strand	213-225	13	3
β-strand	229	1	5
α-helix	230-237	8
α-helix	243-245	3
α-helix	249-251	3
α-helix	252-262	11
β-strand	266-269	4	5
β-strand	278-280	3	5
β-strand	281-288	8	6
β-strand	293-297	5	7
β-strand	303-307	5	7
α-helix	308-316	9
β-strand	326-330	5	6
β-strand	338-340	3	6
α-helix	341-343	3
β-strand	344-346	3	5
α-helix	347	1
β-strand	351	1	3
α-helix	355-357	3
α-helix	358-368	11
α-helix	372-386	15
α-helix	388-390	3
α-helix	392-396	5
β-strand	400-401	2	3
α-helix	405	1
β-strand	406-412	7	2
α-helix	413-417	5
β-strand	418-419	2	8
β-strand	427-428	2	8
β-strand	431	1	9
β-strand	434	1	9
β-strand	444	1	10
β-strand	448	1	11
β-strand	451-455	5	12
α-helix	464-481	18
β-strand	485	1	11
β-strand	491-494	4	12
α-helix	498-500	3
α-helix	501-511	11
β-strand	517-522	6	12
α-helix	527-538	12
β-strand	544-548	5	12
α-helix	549-553	5
α-helix	557-570	14
β-strand	574	1	10
β-strand	577-578	2	8
α-helix	580-582	3
α-helix	585-588	4
β-strand	591-599	9	2
α-helix	609	1
β-strand	610-617	8	2
β-strand	625-632	8	2
α-helix	642-657	16
β-strand	663-669	7	2
α-helix	673-675	3
α-helix	676-694	19
β-strand	701-708	8	2
β-strand	715-717	3	2
α-helix	720-722	3
β-strand	724	1	13
β-strand	729	1	13
α-helix	730-731	2
β-strand	734-736	3	2
β-strand	745	1	1
β-strand	747-751	5	2
α-helix	762	1
β-strand	763-770	8	2
α-helix	776-786	11
β-strand	795	1	9
α-helix	801-816	16
α-helix	839-845	7
α-helix	847-849	3
α-helix	850-853	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-2	A	protein	859	Homo sapiens	Q9UKV8 (AlphaFold model)
fully modified siRNA with a 5' phenylpropargyl phosphate	B	RNA	21	synthetic construct

Sequence of entity 1 (A), FASTA

>9OBD_1 Protein argonaute-2 (chains A)
MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELD
IKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLP
GEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRS
FFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDF
KSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQES
GQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQ
TSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILY
GGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRD
AGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVL
GMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTH
PPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFK
PTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDK
NERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQ
ILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDAAEGDHTDGQANGRDHQ
ALAKAVQVHQDTLRTMYFA

Sequence of entity 2 (B), FASTA

>9OBD_2 fully modified siRNA with a 5' phenylpropargyl phosphate (chains B)
XXGXXUGUGXCXAUGXUGUUX

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
IPH	Phenol	C6 H6 O	3
IPA	Isopropyl alcohol	C3 H8 O	2

Primary citation

Discovery of Argonaute2 compatible 5'-Alkylated phosphate stabilization chemistry for siRNA guide strand. Gebert, L.F.R., MacRae, I.J. To be published.

Other PDB entries of the same protein (UniProt Q9UKV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BF2 1.59 Å, MID domain of Ago2 bound to UMP
4Z4D 1.6 Å, Human Argonaute2 Bound to t1-G Target RNA
3LUC 1.69 Å, Crystal structure of MID domain from hAGO2
3LUK 1.7 Å, Crystal structure of MID domain from hAGO2
7C6B 1.7 Å, Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine…
9LSN 1.75 Å, hAGO2-MID in complex with a chemical modified uridine monophosphate
9BF0 1.78 Å, MID domain of human Argo2 bound to UTP
3LUJ 1.8 Å, Crystal structure of MID domain from hAGO2 in complex with UMP
4Z4E 1.8 Å, Human Argonaute2 Bound to t1-U Target RNA
9LMZ 1.8 Å, hAGO2-MID in complex with a chemical modified uridine monophosphate
4W5O 1.8 Å, The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing…
3LUG 1.85 Å, Crystal structure of MID domain from hAGO2 in complex with CMP

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