6RA4: Human argonaute-2 paz domain

Human argonaute-2 paz domain (214-347) in complex with cgugacucu. Determined by X-ray diffraction at 1.9 Å resolution. Released 8 May 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,590
Mol. weight: 37.44 kDa
Released: 8 May 2019

Explore 6RA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RA4 contains 21 α-helices and 22 β-strands across 2 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	216	1	1
α-helix	217-219	3
β-strand	221	1	2
α-helix	222-230	9
α-helix	235-237	3
α-helix	241-243	3
α-helix	244-254	11
β-strand	258-261	4	2
β-strand	270-272	3	2
β-strand	273-276	4	3
β-strand	285-287	3	4
β-strand	297-299	3	4
α-helix	300-306	7
β-strand	319-322	4	3
α-helix	325-327	3
β-strand	329-332	4	3
α-helix	333-335	3
β-strand	336-338	3	2
α-helix	339	1
α-helix	342	1
β-strand	343	1	1
α-helix	344	1

Chain B: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	215-216	2	5
α-helix	217-219	3
β-strand	221	1	6
α-helix	222-229	8
α-helix	235-237	3
α-helix	241-243	3
α-helix	244-254	11
β-strand	258-261	4	6
β-strand	270-272	3	6
β-strand	273-276	4	7
β-strand	285-288	4	8
β-strand	296-299	4	8
α-helix	300-308	9
β-strand	319-322	4	7
α-helix	325-327	3
β-strand	329-332	4	7
α-helix	333-335	3
β-strand	336-338	3	6
α-helix	339	1
α-helix	342	1
β-strand	343-344	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-2	A, B	protein	136	Homo sapiens	Q9UKV8 (AlphaFold model)
RNA (5'-r(cpgpupgpapcpupcp*u)-3')	L, M	RNA	9	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6RA4_1 Protein argonaute-2 (chains A, B)
GPTAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKY
RVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYL
PLEVCNIVAGQRCIKK

Sequence of entity 2 (L, M), FASTA

>6RA4_2 RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3') (chains L, M)
CGUGACUCU

Primary citation

How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection. Greenidge, P.A., Blommers, M.J.J., Priestle, J.P. et al. J Chem Inf Model (2019) 59:1897-1908. DOI 10.1021/acs.jcim.8b00892 · 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
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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