J3_9DP7_023

3D structure

PDB id

9DP7 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II

Experimental method

ELECTRON MICROSCOPY

Resolution

2.38 Å

Loop

Sequence

UAGAUG*CAUAGCAGG*CGAAUUGCAAUGUCA

Length

30 nucleotides

Bulged bases

9DP7|1|A1|A|3172, 9DP7|1|A1|G|3173, 9DP7|1|A1|A|3215, 9DP7|1|A1|G|3216, 9DP7|1|A1|C|3217, 9DP7|1|A1|G|3219, 9DP7|1|A1|A|3268, 9DP7|1|A1|U|3270, 9DP7|1|A1|C|3272

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

9DP7|1|A1|U|3171
9DP7|1|A1|A|3172
9DP7|1|A1|G|3173
9DP7|1|A1|A|3174
9DP7|1|A1|U|3175
9DP7|1|A1|G|3176
*
9DP7|1|A1|C|3212
9DP7|1|A1|A|3213
9DP7|1|A1|U|3214
9DP7|1|A1|A|3215
9DP7|1|A1|G|3216
9DP7|1|A1|C|3217
9DP7|1|A1|A|3218
9DP7|1|A1|G|3219
9DP7|1|A1|G|3220
*
9DP7|1|A1|C|3265
9DP7|1|A1|G|3266
9DP7|1|A1|A|3267
9DP7|1|A1|A|3268
9DP7|1|A1|U|3269
9DP7|1|A1|U|3270
9DP7|1|A1|G|3271
9DP7|1|A1|C|3272
9DP7|1|A1|A|3273
9DP7|1|A1|A|3274
9DP7|1|A1|U|3275
9DP7|1|A1|G|3276
9DP7|1|A1|U|3277
9DP7|1|A1|C|3278
9DP7|1|A1|A|3279

Current chains

Chain A1

25S rRNA

Nearby chains

Chain AE

60S ribosomal protein L6-A

Chain AM

60S ribosomal protein L14-A

Chain AO

60S ribosomal protein L16-A

Chain AP

60S ribosomal protein L17-A

Chain Af

60S ribosomal protein L33-A