J4_9JPO_004

3D structure

PDB id

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

Description

Structure of the Bacterial Ribosome with human tRNA Lys(mcm5h2U34) and mRNA(AAA)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.18 Å

Loop

Sequence

AUA(2MG)*CA(PSU)*AGG(G7M)(H2U)(5MC)(5MC)*GU

Length

16 nucleotides

Bulged bases

9JPO|1|V|U|8, 9JPO|1|V|H2U|47, 9JPO|1|V|5MC|48

QA status

Modified nucleotides: 2MG, PSU, G7M, 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_9JPO_004 not in the Motif Atlas

Homologous match to J4_6UFM_001

Geometric discrepancy: 0.1774

The information below is about J4_6UFM_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.1

Basepair signature

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

Number of instances in this motif group

48

Unit IDs

9JPO|1|V|A|7
9JPO|1|V|U|8
9JPO|1|V|A|9
9JPO|1|V|2MG|10
*
9JPO|1|V|C|25
9JPO|1|V|A|26
9JPO|1|V|PSU|27
*
9JPO|1|V|A|43
9JPO|1|V|G|44
9JPO|1|V|G|45
9JPO|1|V|G7M|46
9JPO|1|V|H2U|47
9JPO|1|V|5MC|48
9JPO|1|V|5MC|49
*
9JPO|1|V|G|65
9JPO|1|V|U|66

Current chains

Chain V

A-site tRNA-Lys

Nearby chains

Chain A

Small subunit ribosomal RNA; SSU rRNA

Chain a

Large subunit ribosomal RNA; LSU rRNA