J5_8CDR_003

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

CGAG*CGUAA*UGAACGUAG*CGA*UAAGAG

Length

27 nucleotides

Bulged bases

8CDR|1|AA|U|719, 8CDR|1|AA|A|784, 8CDR|1|AA|G|785

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

J5_8CDR_003 not in the Motif Atlas

Homologous match to J5_8P9A_012

Geometric discrepancy: 0.0634

The information below is about J5_8P9A_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_56629.1

Basepair signature

cWW-F-F-tSS-F-cWW-cWW-F-F-cWW-F-cWW-F-F-F-F-F-F

Number of instances in this motif group

3

Unit IDs

8CDR|1|AA|C|675
8CDR|1|AA|G|676
8CDR|1|AA|A|677
8CDR|1|AA|G|678
*
8CDR|1|AA|C|702
8CDR|1|AA|G|703
8CDR|1|AA|U|704
8CDR|1|AA|A|705
8CDR|1|AA|A|706
*
8CDR|1|AA|U|713
8CDR|1|AA|G|714
8CDR|1|AA|A|715
8CDR|1|AA|A|716
8CDR|1|AA|C|717
8CDR|1|AA|G|718
8CDR|1|AA|U|719
8CDR|1|AA|A|720
8CDR|1|AA|G|721
*
8CDR|1|AA|C|749
8CDR|1|AA|G|750
8CDR|1|AA|A|751
*
8CDR|1|AA|U|782
8CDR|1|AA|A|783
8CDR|1|AA|A|784
8CDR|1|AA|G|785
8CDR|1|AA|A|786
8CDR|1|AA|G|787

Current chains

Chain AA

25S ribosomal RNA

Nearby chains

Chain C

60S ribosomal protein L18-A

Chain GG

60S ribosomal protein L4-A

Chain M

60S ribosomal protein L28

Chain N

60S ribosomal protein L29

Chain OO

60S ribosomal protein L13-A

Chain U

60S ribosomal protein L36-A