Named motif workflow FR3D validation passed

Sarcin-ricin motif

A formal seven-nucleotide interaction graph projected into RNAdex, then validated from atomic coordinates with official FR3D interaction and geometric criteria.

View validated structures All examples

Definition and RNAdex query

Literature definition

The formal core has two strands, X1-X4 and Y1-Y3, with five backbone links, four specified non-Watson-Crick base pairs, and four specified stacking interactions.

Candidate query

RNAdex Stage 1 retains the five backbone links and four generic non-WC edges. A composition filter then requires the published core sequence space (A/G)GUA/(A/G)AA.

Retrieval funnel

224,796 WC-bounded RNAdex internal-loop search pool
3,399 Seven-node projected-graph candidates
2,750 Candidates in the formal core sequence space
3 High-confidence canonical SRM representatives

Reproducible workflow

Define

Use the published seven-node graph rather than a motif name or a short sequence alone.

Retrieve

Search RNAdex internal loops for the projected backbone and generic non-WC topology.

Filter

Retain candidates compatible with the published (A/G)GUA/(A/G)AA core sequence space.

Validate

Atomic coordinates were reannotated with official FR3D Python. The complete St-Onge seven-nucleotide interaction signature and the published FR3D five-nucleotide geometric cutoff were both required.

Acceptance mechanism

  • RNAdex internal loop bounded by two canonical WC pairs.
  • All four formal Leontis-Westhof base pairs detected by FR3D.
  • All four formal stacking interactions detected by FR3D.
  • Five-nucleotide FR3D discrepancy to 1JJ2 is at most 0.5.

Reference: Classical H. marismortui sarcin-ricin loop diagnostic core (1JJ2); official FR3D Python commit ed850c00df.

High-confidence canonical representatives

Structure Context RNAdex residues FR3D evidence Download
1F84
AGUA/GAA 		HCV IRES domain IIId solution structure A6, A7, A8, A9, A22, A23, A24 All interaction checks passed
discrepancy 0.437 ≤ 0.5
X1-Y3 tHH X2-X3 cSH X3-Y2 tWH X4-Y1 tHS X1-X3 s55 X2-Y1 s33 X4-Y2 s55 Y2-Y3 s35
PDB file
1JBR
AGUA/GAA 		Restrictocin-bound sarcin-ricin domain RNA C9, C10, C11, C12, F19, F20, F21 All interaction checks passed
discrepancy 0.158 ≤ 0.5
X1-Y3 tHH X2-X3 cSH X3-Y2 tWH X4-Y1 tHS X1-X3 s55 X2-Y1 s33 X4-Y2 s55 Y2-Y3 s35
PDB file
1K73
AGUA/GAA 		23S rRNA occurrence matching the published formal core A212, A213, A214, A215, A225, A226, A227 All interaction checks passed
discrepancy 0.228 ≤ 0.5
X1-Y3 tHH X2-X3 cSH X3-Y2 tWH X4-Y1 tHS X1-X3 s55 X2-Y1 s33 X4-Y2 s55 Y2-Y3 s35
PDB file

Data and validation evidence

Candidate records (CSV)
Confirmed structures (ZIP)
Workflow summary (JSON)
FR3D validation evidence (JSON)
Deterministic candidate audit (CSV)

Primary sources