J5_9VTH_009

3D structure

PDB id

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

Description

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S and initiator tRNA

Experimental method

ELECTRON MICROSCOPY

Resolution

4.7 Å

Loop

Sequence

GCAAAAUGG*UG*UG*CGGACAAGG*CAC

Length

25 nucleotides

Bulged bases

9VTH|1|14|G|2120, 9VTH|1|14|G|2125

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

J5_9VTH_009 not in the Motif Atlas

Homologous match to J5_9PN5_004

Geometric discrepancy: 0.0707

The information below is about J5_9PN5_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_99177.4

Basepair signature

cWW-F-F-F-cWW-F-F-F-F-F-F-F-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

12

Unit IDs

9VTH|1|14|G|1912
9VTH|1|14|C|1913
9VTH|1|14|A|1914
9VTH|1|14|A|1915
9VTH|1|14|A|1916
9VTH|1|14|A|1917
9VTH|1|14|U|1918
9VTH|1|14|G|1919
9VTH|1|14|G|1920
*
9VTH|1|14|U|1944
9VTH|1|14|G|1945
*
9VTH|1|14|U|2113
9VTH|1|14|G|2114
*
9VTH|1|14|C|2118
9VTH|1|14|G|2119
9VTH|1|14|G|2120
9VTH|1|14|A|2121
9VTH|1|14|C|2122
9VTH|1|14|A|2123
9VTH|1|14|A|2124
9VTH|1|14|G|2125
9VTH|1|14|G|2126
*
9VTH|1|14|C|2334
9VTH|1|14|A|2335
9VTH|1|14|C|2336

Current chains

Chain 14

25S rRNA

Nearby chains

Chain LC

60S ribosomal protein L3

Chain LH

60S ribosomal protein L23

Chain LW

Ribosomal protein L19

Chain La

60S ribosomal protein L24