J4_9YDC_011

3D structure

PDB id

9YDC (explore in PDB, NAKB, or RNA 3D Hub)

Description

Eukaryotic 80S ribosome with A/P, P/E tRNAs from uL16 P-site loop mutants in bypass condition

Experimental method

ELECTRON MICROSCOPY

Resolution

3.02 Å

Loop

Sequence

AAG*CGAAAG*CCAUAAACUAUG*UU

Length

23 nucleotides

Bulged bases

9YDC|1|E|A|623, 9YDC|1|E|A|1026, 9YDC|1|E|U|1029, 9YDC|1|E|U|1031

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

J4_9YDC_011 not in the Motif Atlas

Homologous match to J4_9SUM_012

Geometric discrepancy: 0.0833

The information below is about J4_9SUM_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_14595.4

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-cWW-F

Number of instances in this motif group

7

Unit IDs

9YDC|1|E|A|622
9YDC|1|E|A|623
9YDC|1|E|G|624
*
9YDC|1|E|C|975
9YDC|1|E|G|976
9YDC|1|E|A|977
9YDC|1|E|A|978
9YDC|1|E|A|979
9YDC|1|E|G|980
*
9YDC|1|E|C|1021
9YDC|1|E|C|1022
9YDC|1|E|A|1023
9YDC|1|E|U|1024
9YDC|1|E|A|1025
9YDC|1|E|A|1026
9YDC|1|E|A|1027
9YDC|1|E|C|1028
9YDC|1|E|U|1029
9YDC|1|E|A|1030
9YDC|1|E|U|1031
9YDC|1|E|G|1032
*
9YDC|1|E|U|1103
9YDC|1|E|U|1104

Current chains

Chain E

18S rRNA

Nearby chains

Chain A

Large subunit ribosomal RNA; LSU rRNA

Chain Lp

60S ribosomal protein L41-A

Chain SX

40S ribosomal protein S11-A

Chain SY

40S ribosomal protein S13

Chain SZ

40S ribosomal protein S14-B

Chain Sb

40S ribosomal protein S22-A

Chain Sc

40S ribosomal protein S23-A

Chain Se

Small ribosomal subunit protein eS26B