J3_8ZDD_011

3D structure

PDB id

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

Description

Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 (without NOB1)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.7 Å

Loop

Sequence

CCGGAC*GGGUG*UUAGAUG

Length

18 nucleotides

Bulged bases

8ZDD|1|2|G|1274, 8ZDD|1|2|G|1507, 8ZDD|1|2|U|1509

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_8ZDD_011 not in the Motif Atlas

Homologous match to J3_8C3A_041

Geometric discrepancy: 0.19

The information below is about J3_8C3A_041

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_23728.1

Basepair signature

cWW-tWH-F-F-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

2

Unit IDs

8ZDD|1|2|C|1272
8ZDD|1|2|C|1273
8ZDD|1|2|G|1274
8ZDD|1|2|G|1275
8ZDD|1|2|A|1276
8ZDD|1|2|C|1277
*
8ZDD|1|2|G|1320
8ZDD|1|2|G|1321
8ZDD|1|2|G|1322
8ZDD|1|2|U|1323
8ZDD|1|2|G|1324
*
8ZDD|1|2|U|1504
8ZDD|1|2|U|1505
8ZDD|1|2|A|1506
8ZDD|1|2|G|1507
8ZDD|1|2|A|1508
8ZDD|1|2|U|1509
8ZDD|1|2|G|1510

Current chains

Chain 2

18S rRNA

Nearby chains

Chain K

Small ribosomal subunit protein eS10

Chain d

Small ribosomal subunit protein uS14

Chain u

Pre-rRNA-processing protein TSR1 homolog