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
GACACCACAAAA*UGAAAAUGGAUGGCGC
Length
28 nucleotides
Bulged bases
8YLD|1|A|C|1196, 8YLD|1|A|A|1302, 8YLD|1|A|U|1305, 8YLD|1|A|G|1306
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
IL_8YLD_135 not in the Motif Atlas
Homologous match to IL_8P9A_280
Geometric discrepancy: 0.1501
The information below is about IL_8P9A_280
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
IL_34501.1
Basepair signature
cWW-tSH-tHH-L-R-L-R-L-R-L-R-L-R-L-R-L-cWW-L-cWW
Number of instances in this motif group
4

Unit IDs

8YLD|1|A|G|1194
8YLD|1|A|A|1195
8YLD|1|A|C|1196
8YLD|1|A|A|1197
8YLD|1|A|C|1198
8YLD|1|A|C|1199
8YLD|1|A|A|1200
8YLD|1|A|C|1201
8YLD|1|A|A|1202
8YLD|1|A|A|1203
8YLD|1|A|A|1204
8YLD|1|A|A|1205
*
8YLD|1|A|U|1299
8YLD|1|A|G|1300
8YLD|1|A|A|1301
8YLD|1|A|A|1302
8YLD|1|A|A|1303
8YLD|1|A|A|1304
8YLD|1|A|U|1305
8YLD|1|A|G|1306
8YLD|1|A|G|1307
8YLD|1|A|A|1308
8YLD|1|A|U|1309
8YLD|1|A|G|1310
8YLD|1|A|G|1311
8YLD|1|A|C|1312
8YLD|1|A|G|1313
8YLD|1|A|C|1314

Current chains

Chain A
25S rRNA

Nearby chains

Chain B
5S ribosomal RNA; 5S rRNA
Chain E
Large ribosomal subunit protein uL3
Chain I
Large ribosomal subunit protein uL30A
Chain L
Large ribosomal subunit protein uL16
Chain Q
Large ribosomal subunit protein uL13A
Chain h
Large ribosomal subunit protein eL33A
Chain o
Large ribosomal subunit protein eL40A

Coloring options:


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