8AML | pdb_00008aml

Crystal structure of AUGUGGCAU duplex with cadmium ions

• PDB DOI: https://doi.org/10.2210/pdb8AML/pdb
• NAKB: 8AML

• Classification: RNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-08-03 Released: 2022-11-23 
• Deposition Author(s): Kiliszek, A., Rypniewski, W.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.

Kiliszek, A., Pluta, M., Bejger, M., Rypniewski, W.

(2022) RNA 29: 44-54

• PubMed: 36319090 
• DOI: https://doi.org/10.1261/rna.079414.122
• Primary Citation Related Structures: 
  8AMG, 8AMI, 8AMJ, 8AMK, 8AML, 8AMM, 8AMN


• PubMed Abstract: 
  

  The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing a noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba ²⁺ ions. Crystallographic research has shown that two Ba ²⁺ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba ²⁺ , an unusual noncanonical G( syn )-G( syn ) pair is observed instead of the common G( anti )-G( syn ). We further elucidated the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba ²⁺ cations and point to possible applications of this metal-binding propensity.

---

Organizational Affiliation: 
• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Biological assembly 8 assigned by authors.

Biological Assembly 9  

Biological assembly 9 assigned by authors.

Biological Assembly 10  

Biological assembly 10 assigned by authors.

Biological Assembly 11  

Biological assembly 11 assigned by authors.

Biological Assembly 12  

Biological assembly 12 assigned by authors.

Biological Assembly 13  

Biological assembly 13 assigned by authors.

Biological Assembly 14  

Biological assembly 14 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.77 kDa 
• Atom Count: 5,324 
• Modeled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')	A, AA [auth c], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W [auth Y], X [auth Z], Y [auth a], Z [auth b]	9	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD (Subject of Investigation/LOI)	CA [auth F], DA [auth G], EA [auth K]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.193	α = 90
b = 90.6	β = 91.504
c = 139.623	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Kiliszek, A., Rypniewski, W.

---

Funding Organization	Location	Grant Number
Other government	Poland	--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description