4Z4D: Human Argonaute2

Human Argonaute2 Bound to t1-G Target RNA. Determined by X-ray diffraction at 1.6 Å resolution. Released 23 Sept 2015.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 7,654
Mol. weight: 108.23 kDa
Ligands: MG, IPH, IPA
Released: 23 Sept 2015

Explore 4Z4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z4D contains 44 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: 44 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
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
β-strand	93-94	2	4
β-strand	99-102	4	4
β-strand	113-117	5	4
β-strand	128-139	12	4
α-helix	140-147	8
α-helix	156-167	12
α-helix	170-173	4
β-strand	175-177	3	3
β-strand	180-183	4	3
α-helix	184-185	2
β-strand	191-193	3	3
β-strand	196-207	12	3
β-strand	213-225	13	3
β-strand	229	1	5
α-helix	230-238	9
α-helix	243-245	3
α-helix	250-251	2
α-helix	252-262	11
β-strand	266-268	3	5
β-strand	278-280	3	5
β-strand	281-288	8	6
β-strand	293-294	2	7
β-strand	306-307	2	7
α-helix	308-316	9
β-strand	326-330	5	6
β-strand	337-340	4	6
α-helix	341-343	3
β-strand	345-346	2	5
α-helix	347	1
α-helix	350	1
β-strand	351	1	3
α-helix	352	1
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
α-helix	445-447	3
β-strand	448	1	11
β-strand	451-455	5	12
α-helix	464-480	17
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	527-533	7
α-helix	534-540	7
β-strand	544-548	5	12
α-helix	550-553	4
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	600-602	3
α-helix	608-609	2
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
β-strand	763-770	8	2
α-helix	776-786	11
β-strand	795	1	9
α-helix	801-816	16
α-helix	837-846	10
α-helix	847-849	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-2	A	protein	859	Homo sapiens	Q9UKV8 (AlphaFold model)
RNA (5'-r(pupupcpapcpapupupgpcpcpcpapapgpupcpupupu)-3')	B	RNA	21	synthetic construct
RNA (5'-r(cpapapupgpupgpap*g)-3')	D	RNA	11	synthetic construct

Sequence of entity 1 (A), FASTA

>4Z4D_1 Protein argonaute-2 (chains A)
MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELD
IKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLP
GEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRS
FFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDF
KSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQES
GQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQ
TSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILY
GGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRD
AGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVL
GMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTH
PPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFK
PTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDK
NERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQ
ILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQ
ALAKAVQVHQDTLRTMYFA

Sequence of entity 2 (B), FASTA

>4Z4D_2 RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*UP*U)-3') (chains B)
UUCACAUUGCCCAAGUCUCUU

Sequence of entity 3 (D), FASTA

>4Z4D_3 RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*G)-3') (chains D)
CAAUGUGAGAA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
IPH	Phenol	C6 H6 O	4
IPA	Isopropyl alcohol	C3 H8 O	5

Primary citation

Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets. Schirle, N.T., Sheu-Gruttadauria, J., Chandradoss, S.D. et al. Elife (2015) 4. DOI 10.7554/eLife.07646 · PubMed

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
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
6RA4 1.9 Å, Human argonaute-2 paz domain (214-347) in complex with cgugacucu

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