Named motif workflow FR3D validation passed

GNRA tetraloop

A four-nucleotide hairpin sequence search followed by graph and official FR3D interaction and geometric validation.

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Definition and RNAdex query

Literature definition

GNRA denotes a four-nucleotide hairpin loop in which G is the first base, N is any canonical base, R is A or G, and A is the fourth base. The characteristic fold contains a first-to-fourth G-A trans Sugar-Hoogsteen interaction.

Candidate query

Use the RNAdex type search for a hairpin with four unpaired nucleotides, filter the extracted sequence by G[ACGU][AG]A, and retain records with a generic non-WC edge between loop positions one and four.

Retrieval funnel

35,177 Four-nucleotide RNAdex hairpins
16,948 GNRA sequence candidates
15,331 Candidates with first-to-fourth non-WC edge
3 High-confidence canonical GNRA representatives

Reproducible workflow

Type search

Select Hairpin and four unpaired nucleotides. RNAdex internally includes the closing pair in the stored row.

Sequence filter

Retain loop sequences matching G[ACGU][AG]A.

Graph filter

Require a generic non-WC edge between the first G and fourth A.

Validate

Atomic coordinates were reannotated with official FR3D Python. A local five-position reference in PDB 1JJ2 was used with the published FR3D stacking constraints and discrepancy cutoff; stricter cWW and tSH requirements were added for high-confidence canonical assignment.

Acceptance mechanism

  • Four-nucleotide hairpin with GNRA sequence.
  • Strict closing cWW pair and first-to-fourth G-A tSH pair detected by FR3D. These canonical requirements are stricter than the published broad FR3D GNRA search, which allowed a bifurcated closing pair and omitted the tSH constraint.
  • Both stacking constraints from the published FR3D query detected.
  • Five-nucleotide FR3D discrepancy to the 1JJ2 GNRA is at most 0.8.

Reference: C(GAAA)G hairpin used as the local geometric reference; the published FR3D query used the corresponding motif in 1S72 (1JJ2); official FR3D Python commit ed850c00df.

High-confidence canonical representatives

Structure Context RNAdex residues FR3D evidence Download
2JYJ
GAAA 		GAAA tetraloop in an NMR-refined tetraloop-receptor complex A20, A21, A22, A23 All interaction checks passed
discrepancy 0.387 ≤ 0.8
closing pair cWW loop G-A tSH closing5-loop1 s35 loop3-loop4 s35
PDB file
5X8R
GAAA 		GAAA tetraloop in the spinach chloroplast 30S subunit a351, a352, a353, a354 All interaction checks passed
discrepancy 0.164 ≤ 0.8
closing pair cWW loop G-A tSH closing5-loop1 s35 loop3-loop4 s35
PDB file
8FLD
GAGA 		GAGA tetraloop in the human nuclear pre-60S subunit D4604, D4605, D4606, D4607 All interaction checks passed
discrepancy 0.179 ≤ 0.8
closing pair cWW loop G-A tSH closing5-loop1 s35 loop3-loop4 s35
PDB file

Data and validation evidence

Graph-filtered candidates (CSV)
Confirmed structures (ZIP)
Workflow summary (JSON)
FR3D validation evidence (JSON)
Deterministic candidate audit (CSV)

Primary sources