J4_8K2D_008

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

CUG*CG*CUUAAGGUAG*UGAAUG

Length

21 nucleotides

Bulged bases

8K2D|1|C1|U|2269, 8K2D|1|C1|U|2314

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

J4_8K2D_008 not in the Motif Atlas

Homologous match to J4_8P9A_018

Geometric discrepancy: 0.2363

The information below is about J4_8P9A_018

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_93343.1

Basepair signature

cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F

Number of instances in this motif group

4

Unit IDs

8K2D|1|C1|C|2192
8K2D|1|C1|U|2193
8K2D|1|C1|G|2194
*
8K2D|1|C1|C|2248
8K2D|1|C1|G|2249
*
8K2D|1|C1|C|2267
8K2D|1|C1|U|2268
8K2D|1|C1|U|2269
8K2D|1|C1|A|2270
8K2D|1|C1|A|2271
8K2D|1|C1|G|2272
8K2D|1|C1|G|2273
8K2D|1|C1|U|2274
8K2D|1|C1|A|2275
8K2D|1|C1|G|2276
*
8K2D|1|C1|U|2310
8K2D|1|C1|G|2311
8K2D|1|C1|A|2312
8K2D|1|C1|A|2313
8K2D|1|C1|U|2314
8K2D|1|C1|G|2315

Current chains

Chain C1

23S rRNA

Nearby chains

Chain C2

Small subunit ribosomal RNA; SSU rRNA

Chain CE

Eukaryotic translation initiation factor 5A-1

Chain LA

Large ribosomal subunit protein uL2A

Chain Ln

Large ribosomal subunit protein eL41A