8CLM | pdb_00008clm

1.80 A crystal structure of RNA/2'-O-methyl-RNA heteroduplex

• PDB DOI: https://doi.org/10.2210/pdb8CLM/pdb
• NAKB: 8CLM

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


• Deposited: 2023-02-16 Released: 2023-03-01 
• Deposition Author(s): Dolot, R.M., Maciaszek, A., Nawrot, B.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.256 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.199 (DCC) 

Starting Model: experimental

Literature

Crystal structure of RNA/2'-O-methyl-RNA heteroduplex

Dolot, R.M., Maciaszek, A., Mikolajczyk, B., Nawrot, B.C.

To be published.

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.

Macromolecule Content 

• Total Structure Weight: 17.38 kDa 
• Atom Count: 1,481 
• Modeled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*G*UP*CP*UP*CP*CP*UP*AP*GP*)-3')	A, C [auth B], E [auth C]	9	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(UZL)*(OMU)P*(A2M)P*(OMG)P*(OMG)P*(A2M)P*(OMG)P*(A2M)P*(OMC)P*)-3')	B [auth D], D [auth E], F	9	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	H [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.256 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.199 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.103	α = 90
b = 49.303	β = 97.149
c = 55.868	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-01 
Deposition Author(s): Dolot, R.M., Maciaszek, A., Nawrot, B.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-01
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection