J4_9VTH_002

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

AAG*CGAAAG*CCAUAAACGAUG*UU

Length

23 nucleotides

Bulged bases

9VTH|1|11|A|626, 9VTH|1|11|A|1029

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_9VTH_002 not in the Motif Atlas

Homologous match to J4_9PN5_011

Geometric discrepancy: 0.0733

The information below is about J4_9PN5_011

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

9VTH|1|11|A|625
9VTH|1|11|A|626
9VTH|1|11|G|627
*
9VTH|1|11|C|978
9VTH|1|11|G|979
9VTH|1|11|A|980
9VTH|1|11|A|981
9VTH|1|11|A|982
9VTH|1|11|G|983
*
9VTH|1|11|C|1024
9VTH|1|11|C|1025
9VTH|1|11|A|1026
9VTH|1|11|U|1027
9VTH|1|11|A|1028
9VTH|1|11|A|1029
9VTH|1|11|A|1030
9VTH|1|11|C|1031
9VTH|1|11|G|1032
9VTH|1|11|A|1033
9VTH|1|11|U|1034
9VTH|1|11|G|1035
*
9VTH|1|11|U|1106
9VTH|1|11|U|1107

Current chains

Chain 11

18S rRNA

Nearby chains

Chain Lo

60s ribosomal protein l41-like

Chain Lq

60S ribosomal protein L37a

Chain SF

Small ribosomal subunit protein uS8c

Chain SI

40S ribosomal protein S14-2

Chain SJ

40S ribosomal protein S23

Chain SM

40S ribosomal protein S13

Chain SN

40S ribosomal protein S11

Chain Sb

40S ribosomal protein S26