IL_5JUP_140

3D structure

PDB id

5JUP (explore in PDB, NAKB, or RNA 3D Hub)

Description

Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure II (mid-rotated 40S subunit)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.5 Å

Loop

Sequence

GAGUG*CUC

Length

8 nucleotides

Bulged bases

5JUP|1|B|A|1263

QA status

Unknown status

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

IL_5JUP_140 not in the Motif Atlas

Geometric match to IL_1MMS_002

Geometric discrepancy: 0.1281

The information below is about IL_1MMS_002

Detailed Annotation

Major groove platform with extra cWW

Broad Annotation

Major groove platform

Motif group

IL_51387.3

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

21

Unit IDs

5JUP|1|B|G|1262
5JUP|1|B|A|1263
5JUP|1|B|G|1264
5JUP|1|B|U|1265
5JUP|1|B|G|1266
*
5JUP|1|B|C|1275
5JUP|1|B|U|1276
5JUP|1|B|C|1277

Current chains

Chain B

25S ribosomal RNA

Nearby chains

Chain P

uL11 (yeast L12)

Chain VA

uL10 (yeast P0)