7C6B: Ago2 MID domain

Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate. Determined by X-ray diffraction at 1.7 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,520
Mol. weight: 48.03 kDa
Ligands: K2R, PO4
Released: 25 Nov 2020

Explore 7C6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7C6B contains 28 α-helices and 18 β-strands across 3 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	442-443	2
β-strand	448	1	1
β-strand	451-455	5	2
α-helix	464-480	17
α-helix	484	1
β-strand	485	1	1
α-helix	486	1
β-strand	491-494	4	2
α-helix	498-500	3
α-helix	501-511	11
β-strand	517-522	6	2
α-helix	528-533	6
α-helix	534-540	7
β-strand	544-548	5	2
α-helix	549-553	5
α-helix	557-571	15

Chain B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	442-444	3
β-strand	448	1	3
β-strand	451-455	5	4
α-helix	464-480	17
α-helix	484	1
β-strand	485	1	3
α-helix	486	1
β-strand	491-494	4	4
α-helix	498-500	3
α-helix	501-511	11
β-strand	517-522	6	4
α-helix	528-533	6
α-helix	534-540	7
β-strand	544-548	5	4
α-helix	550-553	4
α-helix	557-571	15

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	448	1	5
β-strand	451-455	5	6
α-helix	464-480	17
α-helix	484	1
β-strand	485	1	5
α-helix	486	1
β-strand	491-494	4	6
α-helix	498-500	3
α-helix	501-511	11
β-strand	517-522	6	6
α-helix	528-538	11
β-strand	544-548	5	6
α-helix	550-553	4
α-helix	557-571	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-2	A, B, C	protein	139	Homo sapiens	Q9UKV8 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7C6B_1 Protein argonaute-2 (chains A, B, C)
KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGAD
SVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQT
LSNLCLKINVKLGGVNNIL

Ligands and cofactors

ID	Name	Formula	Copies
K2R	3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]puri…	C19 H21 N4 O9 P	3
PO4	Phosphate ion	O4 P	2

Primary citation

siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand. Shinohara, F., Oashi, T., Harumoto, T. et al. RNA (2021) 27:163-173. DOI 10.1261/rna.073783.119 · 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
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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