J4_9VTH_014

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

GU(1MG)(2MG)*C(M2G)C*GAU(7MG)(H2U)(5MC)(5MC)*GC

Length

16 nucleotides

Bulged bases

9VTH|1|16|U|9, 9VTH|1|16|H2U|47, 9VTH|1|16|5MC|48

QA status

Modified nucleotides: 1MG, 2MG, M2G, 7MG, H2U, 5MC

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_014 not in the Motif Atlas

Homologous match to J4_6UFM_001

Geometric discrepancy: 0.2438

The information below is about J4_6UFM_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.3

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

50

Unit IDs

9VTH|1|16|G|8
9VTH|1|16|U|9
9VTH|1|16|1MG|10
9VTH|1|16|2MG|11
*
9VTH|1|16|C|25
9VTH|1|16|M2G|26
9VTH|1|16|C|27
*
9VTH|1|16|G|43
9VTH|1|16|A|44
9VTH|1|16|U|45
9VTH|1|16|7MG|46
9VTH|1|16|H2U|47
9VTH|1|16|5MC|48
9VTH|1|16|5MC|49
*
9VTH|1|16|G|65
9VTH|1|16|C|66

Current chains

Chain 16

tRNA(iMet)

Nearby chains

Chain 11

Small subunit ribosomal RNA; SSU rRNA

Chain 14

Large subunit ribosomal RNA; LSU rRNA

Chain LJ

60S ribosomal protein L10