Remembrances of Things Past

Comparison of RNA conformers with very small RNA crystal structures

• Clustered the conformers• Compared with dinucleoside phosphates

– High resolution– With and without ligands

RMSD Clustering

• Hierarchical clustering using ‘complete linkages’ • Cluster data set included:

– 38 model dinucleotides representing the diversity of RNA conformation space (earlier version)

– 7 high resolution dinucleoside phosphate crystal structures

• Clustered families based on backbone RMSD

RMSD clustering

P-O5’-C5’-C4-’C3-O3’-P-O5’-C5’C4’-C3’-O3’

No base atoms included in calculations

RMSD Cluster Results

ARNA

DRB006CGPF

All A RNA-like conformers

Subtle backbone changes affect base geometry and function

RMSD Cluster Results

URB008UPA2

Cluster 2Cluster 1

UpA 2 an open conformation

UpA 2 like conformers

RMSD Cluster Results

URB003ApA - Ca++

DRB003ApU - 9AA

URB008UPA1

UpA1helix turner

UpA1 like conformerssmall backbone changes make big

structural changes

RMSD Cluster Resultsdinucleotide backbone

ARNADRB006CGPF

URB003ApA - Ca4

DRB003ApU - 9AA

URB008UPA1

URB008UPA2

Cluster 2

Cluster 1

RMSD Cluster Resultssuite backbone

ARNA

DRB006CGPF

URB003ApA - Ca4

DRB003ApU - 9AA

URB008UPA1

URB008UPA2

RMSD Cluster Results backbone plus chi

ARNA

DRB006CGPF URB003

ApA - Ca4

DRB003ApU - 9AAURB008

UPA1

URB008UPA2

myRNAdb

• MySQL relational database of ~1000 RNA containing structures in NDB/PDB

• Uses core schema based on mmCIF/PDB Exchange Dictionary

• Includes base-pair and base-pair step geometries and RNA SCOR annotation

• Warehouse style tables for mining nucleotide, dinucleotide and trinucleotide features.

• Python tools for loading, access and analysis