J5_9VTH_011

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

UUGA*UUUG*CA*UG*CAGAAAA

Length

19 nucleotides

Bulged bases

9VTH|1|14|G|2421, 9VTH|1|14|A|2802, 9VTH|1|14|G|2803, 9VTH|1|14|A|2804, 9VTH|1|14|A|2805

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_011 not in the Motif Atlas

Homologous match to J5_9H3G_006

Geometric discrepancy: 0.1097

The information below is about J5_9H3G_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_96125.4

Basepair signature

cWW-cWH-cWH-tSS-cWW-cWW-cWW-F-cWW

Number of instances in this motif group

8

Unit IDs

9VTH|1|14|U|2419
9VTH|1|14|U|2420
9VTH|1|14|G|2421
9VTH|1|14|A|2422
*
9VTH|1|14|U|2614
9VTH|1|14|U|2615
9VTH|1|14|U|2616
9VTH|1|14|G|2617
*
9VTH|1|14|C|2630
9VTH|1|14|A|2631
*
9VTH|1|14|U|2653
9VTH|1|14|G|2654
*
9VTH|1|14|C|2801
9VTH|1|14|A|2802
9VTH|1|14|G|2803
9VTH|1|14|A|2804
9VTH|1|14|A|2805
9VTH|1|14|A|2806
9VTH|1|14|A|2807

Current chains

Chain 14

25S rRNA

Nearby chains

Chain 10

RNA (204-MER)

Chain LB

60S ribosomal protein L8-like

Chain LI

60s ribosomal protein l27a-3

Chain LU

Ribosomal protein L15

Chain LV

60S ribosomal protein L18-2

Chain LY

60S ribosomal protein L21-1-like

Chain Ld

60S ribosomal protein L29

Chain Lp

60S ribosomal protein L44