9BEZ: MID domain of human Argo2

MID domain of human Argo2 bound to RNA. Determined by X-ray diffraction at 1.9 Å resolution. Released 10 Jul 2024.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,265
Mol. weight: 46.78 kDa
Ligands: A1ANT
Released: 10 Jul 2024

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

Secondary structure: helices and β-sheets

9BEZ contains 24 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.

Chains A and B: 8 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
β-strand	485	1	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	527-534	8
α-helix	535-540	6
β-strand	544-548	5	2
α-helix	550-553	4
α-helix	557-571	15

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	441-443	3
β-strand	448	1	5
β-strand	451-455	5	6
α-helix	464-480	17
β-strand	485	1	5
β-strand	491-494	4	6
α-helix	498-500	3
α-helix	501-511	11
β-strand	517-522	6	6
α-helix	527-534	8
α-helix	535-540	6
β-strand	543-548	6	6
α-helix	550-553	4
α-helix	557-570	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein argonaute-2	A, B, C	protein	136	Homo sapiens	Q9UKV8 (AlphaFold model)

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

>9BEZ_1 Protein argonaute-2 (chains A, B, C)
KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGAD
SVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQT
LSNLCLKINVKLGGVN

Ligands and cofactors

ID	Name	Formula	Copies
A1ANT	[(3~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidan…	C9 H15 N2 O14 P3	3

Primary citation

Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6 -SUMO Tag Removal, Nucleotide Binding, and Crystal Growth. Lei, L., Harp, J.M., Chaput, J.C. et al. Curr Protoc (2024) 4:e1088-e1088. DOI 10.1002/cpz1.1088 · 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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