J4_5AFI_016
3D structure
- PDB id
- 5AFI (explore in PDB, NAKB, or RNA 3D Hub)
- Description
- 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
- Experimental method
- ELECTRON MICROSCOPY
- Resolution
- 2.9 Å
Loop
- Sequence
- A(4SU)AG*CAG*CGU(7MG)UCC*GU
- Length
- 16 nucleotides
- Bulged bases
- 5AFI|1|y|4SU|8||||P_1, 5AFI|1|y|U|47||||P_1, 5AFI|1|y|C|48||||P_1
- 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_5AFI_016 not in the Motif Atlas
- Homologous match to J4_5WT1_002
- Geometric discrepancy: 0.2265
- The information below is about J4_5WT1_002
- Detailed Annotation
- tRNA junction
- Broad Annotation
- No text annotation
- Motif group
- J4_40477.1
- Basepair signature
- cWW-F-cWW-F-cWW-cHW-F-F-F-cWW-F
- Number of instances in this motif group
- 4
Unit IDs
5AFI|1|y|A|7||||P_1
5AFI|1|y|4SU|8||||P_1
5AFI|1|y|A|9||||P_1
5AFI|1|y|G|10||||P_1
*
5AFI|1|y|C|25||||P_1
5AFI|1|y|A|26||||P_1
5AFI|1|y|G|27||||P_1
*
5AFI|1|y|C|43||||P_1
5AFI|1|y|G|44||||P_1
5AFI|1|y|U|45||||P_1
5AFI|1|y|7MG|46||||P_1
5AFI|1|y|U|47||||P_1
5AFI|1|y|C|48||||P_1
5AFI|1|y|C|49||||P_1
*
5AFI|1|y|G|65||||P_1
5AFI|1|y|U|66||||P_1
Current chains
- Chain y
- A/T-site Phe-tRNAPhe
Nearby chains
- Chain A
- Large subunit ribosomal RNA; LSU rRNA
- Chain a
- Small subunit ribosomal RNA; SSU rRNA
- Chain l
- 30S ribosomal protein S12
- Chain z
- Elongation factor Tu 2
Coloring options: