3D structure

PDB id
8YLD (explore in PDB, NAKB, or RNA 3D Hub)
Description
State 4a (S4a) of yeast 80S ribosome bound to 2 tRNAs and open eEF3 and eEF2 during translocation
Experimental method
ELECTRON MICROSCOPY
Resolution
3.9 Å

Loop

Sequence
UUGA*UUUG*CA*UG*CAGAAAA
Length
19 nucleotides
Bulged bases
8YLD|1|A|G|2418, 8YLD|1|A|A|2799, 8YLD|1|A|G|2800, 8YLD|1|A|A|2801, 8YLD|1|A|A|2802, 8YLD|1|A|A|2803
QA status
Valid loop

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
J5_8YLD_013 not in the Motif Atlas
Homologous match to J5_8C3A_006
Geometric discrepancy: 0.109
The information below is about J5_8C3A_006
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
Not in a motif group
Basepair signature
Not available
Number of instances in this motif group
0

Unit IDs

8YLD|1|A|U|2416
8YLD|1|A|U|2417
8YLD|1|A|G|2418
8YLD|1|A|A|2419
*
8YLD|1|A|U|2611
8YLD|1|A|U|2612
8YLD|1|A|U|2613
8YLD|1|A|G|2614
*
8YLD|1|A|C|2627
8YLD|1|A|A|2628
*
8YLD|1|A|U|2650
8YLD|1|A|G|2651
*
8YLD|1|A|C|2798
8YLD|1|A|A|2799
8YLD|1|A|G|2800
8YLD|1|A|A|2801
8YLD|1|A|A|2802
8YLD|1|A|A|2803
8YLD|1|A|A|2804

Current chains

Chain A
25S rRNA

Nearby chains

Chain D
Large ribosomal subunit protein uL2A
Chain P
Large ribosomal subunit protein eL15A
Chain S
Large ribosomal subunit protein eL18A
Chain V
Large ribosomal subunit protein eL21A
Chain c
Large ribosomal subunit protein uL15
Chain d
Large ribosomal subunit protein eL29
Chain q
Large ribosomal subunit protein eL42A
Chain t
Transfer RNA; tRNA

Coloring options:


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