J5_9VTH_003

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

CAUG*CGAAUGGC*GAG*CAC*GGCAG

Length

23 nucleotides

Bulged bases

9VTH|1|11|A|94, 9VTH|1|11|C|428

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_003 not in the Motif Atlas

Homologous match to J5_9PN5_009

Geometric discrepancy: 0.1088

The information below is about J5_9PN5_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_58574.4

Basepair signature

cWW-F-tSS-cSS-F-cWW-cWW-cWW-F-F-cWW-F-F-cWW-cWW

Number of instances in this motif group

7

Unit IDs

9VTH|1|11|C|54
9VTH|1|11|A|55
9VTH|1|11|U|56
9VTH|1|11|G|57
*
9VTH|1|11|C|91
9VTH|1|11|G|92
9VTH|1|11|A|93
9VTH|1|11|A|94
9VTH|1|11|U|95
9VTH|1|11|G|96
9VTH|1|11|G|97
9VTH|1|11|C|98
*
9VTH|1|11|G|390
9VTH|1|11|A|391
9VTH|1|11|G|392
*
9VTH|1|11|C|413
9VTH|1|11|A|414
9VTH|1|11|C|415
*
9VTH|1|11|G|426
9VTH|1|11|G|427
9VTH|1|11|C|428
9VTH|1|11|A|429
9VTH|1|11|G|430

Current chains

Chain 11

18S rRNA

Nearby chains

Chain LH

60S ribosomal protein L23

Chain SC

40S ribosomal protein S9-2-like

Chain SQ

40S ribosomal protein S4

Chain SR

40S ribosomal protein S6

Chain ST

40S ribosomal protein S8

Chain SZ

40S ribosomal protein S24