3D structure

PDB id
8K2D (explore in PDB, NAKB, or RNA 3D Hub)
Description
Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A
Experimental method
ELECTRON MICROSCOPY
Resolution
3.2 Å

Loop

Sequence
GGAGUC*GGAC*GUUC*GC*GCAGAUC
Length
23 nucleotides
Bulged bases
8K2D|1|C1|U|1436
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_8K2D_002 not in the Motif Atlas
Homologous match to J5_8C3A_002
Geometric discrepancy: 0.0611
The information below is about J5_8C3A_002
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

8K2D|1|C1|G|658
8K2D|1|C1|G|659
8K2D|1|C1|A|660
8K2D|1|C1|G|661
8K2D|1|C1|U|662
8K2D|1|C1|C|663
*
8K2D|1|C1|G|799
8K2D|1|C1|G|800
8K2D|1|C1|A|801
8K2D|1|C1|C|802
*
8K2D|1|C1|G|941
8K2D|1|C1|U|942
8K2D|1|C1|U|943
8K2D|1|C1|C|944
*
8K2D|1|C1|G|1375
8K2D|1|C1|C|1376
*
8K2D|1|C1|G|1431
8K2D|1|C1|C|1432
8K2D|1|C1|A|1433
8K2D|1|C1|G|1434
8K2D|1|C1|A|1435
8K2D|1|C1|U|1436
8K2D|1|C1|C|1437

Current chains

Chain C1
23S rRNA

Nearby chains

Chain C3
5.8S ribosomal RNA; 5.8S rRNA
Chain LC
Large ribosomal subunit protein uL4A
Chain LL
Large ribosomal subunit protein eL13A
Chain LN
Large ribosomal subunit protein eL15A
Chain La
Large ribosomal subunit protein uL15
Chain Le
Large ribosomal subunit protein eL32

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