9J6P | pdb_00009j6p

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

• PDB DOI: https://doi.org/10.2210/pdb9J6P/pdb
• NAKB: 9J6P

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-08-16 Released: 2025-01-15 
• Deposition Author(s): Kondo, J., Nagasawa, R., Onizuka, K., Kawamura, K., Tsuzuki, K., Murase, H., Komatsu, K.R., Miyashita, E., Saito, H., Nagatsugi, F.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.268 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: in silico

Literature

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.

(2025) Chem Commun (Camb) 61: 1120-1123

• PubMed: 39641381 
• DOI: https://doi.org/10.1039/d4cc04677c
• Primary Citation of Related Structures:  
  9J6P


• 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.

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Organizational Affiliation: 
• Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi 980-8577, Japan. [e-mail].
Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan.
Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Miyagi 980-8577, Japan.
Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan. [e-mail].
Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.3 kDa 
• Atom Count: 1,010 
• Modeled Residue Count: 43 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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')	A, B	22	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L3Y (Subject of Investigation/LOI)	C [auth A], D [auth B]	~{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 C22 H32 N6 O7 IOPVLKFMUHLRKC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.268 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.156	α = 90
b = 46.156	β = 90
c = 336.178	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Kondo, J., Nagasawa, R., Onizuka, K., Kawamura, K., Tsuzuki, K., Murase, H., Komatsu, K.R., Miyashita, E., Saito, H., Nagatsugi, F.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121014
Japan Science and Technology	Japan	JPMJFR2002
Japan Science and Technology	Japan	JPMJSP2114

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Database references