ISDA

Deposition Date 2024-08-16

Release Date 2025-01-15

Last Version Date 2025-04-16

Entry Detail

PDB ID:

9J6P

Keywords:

RNA

Title:

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

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.49 Å

R-Value Free:

0.26

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

H 3 2

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule: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')
Chain IDs:A, B
Chain Length:22
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

A1L3Y

Primary Citation

Crystallographic analysis of G-clamp-RNA complex assisted by large scale RNA-binding profile.

Nagasawa, R, Onizuka, K, Kawamura, K, Tsuzuki, K, Murase, H, Komatsu, K.R, Miyashita, E, Saito, H, Kondo, J, Nagatsugi, F.Show

Chem.Commun.(Camb.) 61 1120 1123 (2025)

PMID: 39641381 DOI: 10.1039/d4cc04677c

Abstact

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.

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Primary Citation of related structures