J4_9VVI_005

3D structure

PDB id

9VVI (explore in PDB, NAKB, or RNA 3D Hub)

Description

Cryo-EM structure of SecM-arrested 70S ribosome with YheS

Experimental method

ELECTRON MICROSCOPY

Resolution

2.82 Å

Loop

Sequence

A(4SU)AG*CAC*GGG(G7M)UCG*UU

Length

16 nucleotides

Bulged bases

9VVI|1|Z|4SU|8, 9VVI|1|Z|C|48

QA status

Modified nucleotides: 4SU, G7M

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_9VVI_005 not in the Motif Atlas

Homologous match to J4_7MRL_001

Geometric discrepancy: 0.1567

The information below is about J4_7MRL_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.2

Basepair signature

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

Number of instances in this motif group

49

Unit IDs

9VVI|1|Z|A|7
9VVI|1|Z|4SU|8
9VVI|1|Z|A|9
9VVI|1|Z|G|10
*
9VVI|1|Z|C|25
9VVI|1|Z|A|26
9VVI|1|Z|C|27
*
9VVI|1|Z|G|43
9VVI|1|Z|G|44
9VVI|1|Z|G|45
9VVI|1|Z|G7M|46
9VVI|1|Z|U|47
9VVI|1|Z|C|48
9VVI|1|Z|G|49
*
9VVI|1|Z|U|65
9VVI|1|Z|U|66

Current chains

Chain Z

P-site tRNA (tRNAGly)

Nearby chains

Chain A

Small subunit ribosomal RNA; SSU rRNA

Chain M

Small ribosomal subunit protein uS13

Chain a

Large subunit ribosomal RNA; LSU rRNA