J3_8CDR_032

3D structure

PDB id

8CDR (explore in PDB, NAKB, or RNA 3D Hub)

Description

Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Experimental method

ELECTRON MICROSCOPY

Resolution

2.04 Å

Loop

Sequence

AGAUGG*CGUUUCAAAGG*CACCAU

Length

23 nucleotides

Bulged bases

8CDR|1|AA|C|1556, 8CDR|1|AA|A|1558, 8CDR|1|AA|A|1580, 8CDR|1|AA|C|1581

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

J3_8CDR_032 not in the Motif Atlas

Homologous match to J3_9PN5_015

Geometric discrepancy: 0.203

The information below is about J3_9PN5_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_53783.2

Basepair signature

cWW-tSH-tHW-F-tWW-F-tHS-F-cWW-cWW-F-tWW-F

Number of instances in this motif group

3

Unit IDs

8CDR|1|AA|A|1537
8CDR|1|AA|G|1538
8CDR|1|AA|A|1539
8CDR|1|AA|U|1540
8CDR|1|AA|G|1541
8CDR|1|AA|G|1542
*
8CDR|1|AA|C|1551
8CDR|1|AA|G|1552
8CDR|1|AA|U|1553
8CDR|1|AA|U|1554
8CDR|1|AA|U|1555
8CDR|1|AA|C|1556
8CDR|1|AA|A|1557
8CDR|1|AA|A|1558
8CDR|1|AA|A|1559
8CDR|1|AA|G|1560
8CDR|1|AA|G|1561
*
8CDR|1|AA|C|1579
8CDR|1|AA|A|1580
8CDR|1|AA|C|1581
8CDR|1|AA|C|1582
8CDR|1|AA|A|1583
8CDR|1|AA|U|1584

Current chains

Chain AA

25S ribosomal RNA

Nearby chains

Chain CC

5.8S ribosomal RNA; 5.8S rRNA

Chain EE

60S ribosomal protein L2-A

Chain J

60S ribosomal protein L25

Chain KK

60S ribosomal protein L8-A

Chain QQ

60S ribosomal protein L15-A

Chain V

60S ribosomal protein L37-A