J4_9KDT_013

3D structure

PDB id

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

Description

Cryo-EM structure of 80S ribosome

Experimental method

ELECTRON MICROSCOPY

Resolution

2.63 Å

Loop

Sequence

GUGG*UGC*GAGGUCG*CC

Length

16 nucleotides

Bulged bases

9KDT|1|S7|U|9, 9KDT|1|S7|U|47, 9KDT|1|S7|C|48

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_9KDT_013 not in the Motif Atlas

Homologous match to J4_7EQJ_002

Geometric discrepancy: 0.1832

The information below is about J4_7EQJ_002

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.2

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

49

Unit IDs

9KDT|1|S7|G|8
9KDT|1|S7|U|9
9KDT|1|S7|G|10
9KDT|1|S7|G|11
*
9KDT|1|S7|U|25
9KDT|1|S7|G|26
9KDT|1|S7|C|27
*
9KDT|1|S7|G|43
9KDT|1|S7|A|44
9KDT|1|S7|G|45
9KDT|1|S7|G|46
9KDT|1|S7|U|47
9KDT|1|S7|C|48
9KDT|1|S7|G|49
*
9KDT|1|S7|C|65
9KDT|1|S7|C|66

Current chains

Chain S7

P/P, E/E tRNA

Nearby chains

Chain L5

Large subunit ribosomal RNA; LSU rRNA

Chain LI

Large ribosomal subunit protein uL16-like