IL_8K2D_090

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

GAAUG*CGC

Length

8 nucleotides

Bulged bases

None detected

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_8K2D_090 not in the Motif Atlas

Homologous match to IL_5TBW_087

Geometric discrepancy: 0.5189

The information below is about IL_5TBW_087

Detailed Annotation

Major groove platform with extra pair

Broad Annotation

Major groove platform

Motif group

IL_63450.5

Basepair signature

cWW-cHS-cWW-cWW-cWW

Number of instances in this motif group

7

Unit IDs

8K2D|1|C1|G|2206
8K2D|1|C1|A|2207
8K2D|1|C1|A|2208
8K2D|1|C1|U|2209
8K2D|1|C1|G|2210
*
8K2D|1|C1|C|2235
8K2D|1|C1|G|2236
8K2D|1|C1|C|2237

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 L1

Large ribosomal subunit protein uL1A