J4_4V5P_032

3D structure

PDB id

4V5P (explore in PDB, NAKB, or RNA 3D Hub)

Description

The crystal structure of EF-Tu and A9C-tRNA-Trp bound to a near- cognate codon on the 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.1 Å

Loop

Sequence

G(4SU)CG*CAC*GGU(7MG)UUG*CC

Length

16 nucleotides

Bulged bases

4V5P|1|CY|4SU|8, 4V5P|1|CY|U|47, 4V5P|1|CY|U|48

QA status

Modified nucleotides: 4SU, 7MG

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_4V5P_032 not in the Motif Atlas

Homologous match to J4_5WT1_002

Geometric discrepancy: 0.3101

The information below is about J4_5WT1_002

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_40477.2

Basepair signature

cWW-F-cWW-F-cWW-F-F-F-F-cWW-F

Number of instances in this motif group

4

Unit IDs

4V5P|1|CY|G|7
4V5P|1|CY|4SU|8
4V5P|1|CY|C|9
4V5P|1|CY|G|10
*
4V5P|1|CY|C|25
4V5P|1|CY|A|26
4V5P|1|CY|C|27
*
4V5P|1|CY|G|43
4V5P|1|CY|G|44
4V5P|1|CY|U|45
4V5P|1|CY|7MG|46
4V5P|1|CY|U|47
4V5P|1|CY|U|48
4V5P|1|CY|G|49
*
4V5P|1|CY|C|65
4V5P|1|CY|C|66

Current chains

Chain CY

A-SITE TRNA A9C TRP-TRNA TRP

Nearby chains

Chain CA

Small subunit ribosomal RNA; SSU rRNA

Chain CL

30S RIBOSOMAL PROTEIN S12

Chain CZ

ELONGATION FACTOR TU

Chain DA

Large subunit ribosomal RNA; LSU rRNA