J3_8I9R_008

3D structure

PDB id

8I9R (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP

Experimental method

ELECTRON MICROSCOPY

Resolution

3.1 Å

Loop

Sequence

AUGAAAAGCAC*GGGUUAAAUAGCACG*CU

Length

28 nucleotides

Bulged bases

8I9R|1|C1|U|390, 8I9R|1|C1|A|394

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_8I9R_008 not in the Motif Atlas

Homologous match to J3_8P9A_047

Geometric discrepancy: 0.157

The information below is about J3_8P9A_047

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

8I9R|1|C1|A|361
8I9R|1|C1|U|362
8I9R|1|C1|G|363
8I9R|1|C1|A|364
8I9R|1|C1|A|365
8I9R|1|C1|A|366
8I9R|1|C1|A|367
8I9R|1|C1|G|368
8I9R|1|C1|C|369
8I9R|1|C1|A|370
8I9R|1|C1|C|371
*
8I9R|1|C1|G|382
8I9R|1|C1|G|383
8I9R|1|C1|G|384
8I9R|1|C1|U|385
8I9R|1|C1|U|386
8I9R|1|C1|A|387
8I9R|1|C1|A|388
8I9R|1|C1|A|389
8I9R|1|C1|U|390
8I9R|1|C1|A|391
8I9R|1|C1|G|392
8I9R|1|C1|C|393
8I9R|1|C1|A|394
8I9R|1|C1|C|395
8I9R|1|C1|G|396
*
8I9R|1|C2|C|19
8I9R|1|C2|U|20

Current chains

Chain C1

RNA (3341-MER)

Chain C2

RNA (256-MER)

Nearby chains

Chain Cd

Brix domain-containing protein

Chain Ce

Protein MAK16

Chain LC

60S ribosomal protein L4-like protein

Chain LP

60S ribosomal protein l17-like protein

Chain LY

60S ribosomal protein L26-like protein