IL_9NPY_001

3D structure

PDB id

9NPY (explore in PDB, NAKB, or RNA 3D Hub)

Description

SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome (local refinement of the 40S head)

Experimental method

ELECTRON MICROSCOPY

Resolution

2.1 Å

Loop

Sequence

ACCA*UCCCU

Length

9 nucleotides

Bulged bases

9NPY|1|i|C|1215, 9NPY|1|i|C|1216

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_9NPY_001 not in the Motif Atlas

Geometric match to IL_8CRE_445

Geometric discrepancy: 0.0666

The information below is about IL_8CRE_445

Detailed Annotation

C-loop

Broad Annotation

No text annotation

Motif group

IL_63596.12

Basepair signature

cWW-cWS-cSH-tWH-cWW-L

Number of instances in this motif group

22

Unit IDs

9NPY|1|i|A|1214
9NPY|1|i|C|1215
9NPY|1|i|C|1216
9NPY|1|i|A|1217
*
9NPY|1|i|U|1681
9NPY|1|i|C|1682
9NPY|1|i|C|1683
9NPY|1|i|C|1684
9NPY|1|i|U|1685

Current chains

Chain i

18S ribosomal RNA

Nearby chains

Chain E

40S ribosomal protein uS7, RPS5

Chain Q

40S ribosomal protein uS9, RPS16

Chain c

40S ribosomal protein eS28, RPS28