J3_6XIR_023

3D structure

PDB id

6XIR (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress

Experimental method

ELECTRON MICROSCOPY

Resolution

3.2 Å

Loop

Sequence

CUUAAUUU*GGGGAAACUCAC*GGCCG

Length

25 nucleotides

Bulged bases

6XIR|1|2|G|1199, 6XIR|1|2|G|1201, 6XIR|1|2|A|1203, 6XIR|1|2|A|1204, 6XIR|1|2|C|1205, 6XIR|1|2|U|1206, 6XIR|1|2|C|1457

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_6XIR_023 not in the Motif Atlas

Homologous match to J3_8C3A_040

Geometric discrepancy: 0.5826

The information below is about J3_8C3A_040

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_83516.3

Basepair signature

cWW-F-F-F-tWW-F-tSH-tSS-cSS-F-F-F-F-F-cWW-cWW-F-F-F

Number of instances in this motif group

4

Unit IDs

6XIR|1|2|C|1180
6XIR|1|2|U|1181
6XIR|1|2|U|1182
6XIR|1|2|A|1183
6XIR|1|2|A|1184
6XIR|1|2|U|1185
6XIR|1|2|U|1186
6XIR|1|2|U|1187
*
6XIR|1|2|G|1198
6XIR|1|2|G|1199
6XIR|1|2|G|1200
6XIR|1|2|G|1201
6XIR|1|2|A|1202
6XIR|1|2|A|1203
6XIR|1|2|A|1204
6XIR|1|2|C|1205
6XIR|1|2|U|1206
6XIR|1|2|C|1207
6XIR|1|2|A|1208
6XIR|1|2|C|1209
*
6XIR|1|2|G|1454
6XIR|1|2|G|1455
6XIR|1|2|C|1456
6XIR|1|2|C|1457
6XIR|1|2|G|1458

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain AA

40S ribosomal protein S10-A

Chain AF

RPS15 isoform 1

Chain AG

40S ribosomal protein S16-A

Chain AI

40S ribosomal protein S18-A

Chain AK

RPS20 isoform 1

Chain AT

RPS29A isoform 1

Chain AZ

Transfer RNA; tRNA