J3_9VTH_018

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

AU*AUGAAAAGGAC*GAGUCAAAGAGUGCU

Length

28 nucleotides

Bulged bases

9VTH|1|14|G|395, 9VTH|1|14|G|399

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

J3_9VTH_018 not in the Motif Atlas

Homologous match to J3_9H3G_002

Geometric discrepancy: 0.1009

The information below is about J3_9H3G_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.4

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

11

Unit IDs

9VTH|1|13|A|22
9VTH|1|13|U|23
*
9VTH|1|14|A|366
9VTH|1|14|U|367
9VTH|1|14|G|368
9VTH|1|14|A|369
9VTH|1|14|A|370
9VTH|1|14|A|371
9VTH|1|14|A|372
9VTH|1|14|G|373
9VTH|1|14|G|374
9VTH|1|14|A|375
9VTH|1|14|C|376
*
9VTH|1|14|G|387
9VTH|1|14|A|388
9VTH|1|14|G|389
9VTH|1|14|U|390
9VTH|1|14|C|391
9VTH|1|14|A|392
9VTH|1|14|A|393
9VTH|1|14|A|394
9VTH|1|14|G|395
9VTH|1|14|A|396
9VTH|1|14|G|397
9VTH|1|14|U|398
9VTH|1|14|G|399
9VTH|1|14|C|400
9VTH|1|14|U|401

Current chains

Chain 13

5.8S rRNA

Chain 14

25S rRNA

Nearby chains

Chain LD

60S ribosomal protein L4-like

Chain LL

60S ribosomal protein L17-1 isoform X2

Chain LN

60S ribosomal protein L26-1

Chain Lm

60S ribosomal protein L39-3