9J6P

pre-mir-125a internal loop in complex with G-clamp

This is a non-PDB format compatible entry.

Summary for 9J6P

• Entry DOI: 10.2210/pdb9j6p/pdb
• Descriptor: RNA (5'-R(P*UP*GP*CP*GP*GP*GP*GP*UP*CP*CP*CP*GP*GP*GP*AP*GP*GP*AP*CP*CP*GP*C)-3'), ~{N}-[2-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]ethyl]-2-[9-(2-azanylethoxy)-2-oxidanylidene-10~{H}-pyrimido[5,4-b][1,4]benzoxazin-3-yl]ethanamide (3 entities in total)
• Functional Keywords: micro rna, g-clamp, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 15303.70

Authors

Kondo, J.,Nagasawa, R.,Onizuka, K.,Kawamura, K.,Tsuzuki, K.,Murase, H.,Komatsu, K.R.,Miyashita, E.,Saito, H.,Nagatsugi, F. (deposition date: 2024-08-16, release date: 2025-01-15, Last modification date: 2025-04-16)

Primary citation

Nagasawa, R.,Onizuka, K.,Kawamura, K.,Tsuzuki, K.,Murase, H.,Komatsu, K.R.,Miyashita, E.,Saito, H.,Kondo, J.,Nagatsugi, F.
Crystallographic analysis of G-clamp-RNA complex assisted by large scale RNA-binding profile.
Chem.Commun.(Camb.), 61:1120-1123, 2025

PubMed Abstract: We present the X-ray crystal structure of a complex between a G-clamp and an internal loop motif of pre-mir-125a, selected from high affinity RNAs identified in a large-scale RNA-binding profile. This X-ray crystal structure reveals that the G-clamp interacts with three distinct guanine bases, forming robust bonds through hydrogen bonding and stacking interactions.

PubMed: 39641381
DOI: 10.1039/d4cc04677c

Experimental method

X-RAY DIFFRACTION (2.49 Å)