J4_6ZMI_015

3D structure

PDB id

6ZMI (explore in PDB, NAKB, or RNA 3D Hub)

Description

SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex

Experimental method

ELECTRON MICROSCOPY

Resolution

2.6 Å

Loop

Sequence

AAG*CGAAAG*CCAUAAACGAUG*UU

Length

23 nucleotides

Bulged bases

6ZMI|1|S2|A|672, 6ZMI|1|S2|A|1083, 6ZMI|1|S2|C|1085, 6ZMI|1|S2|A|1087

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_6ZMI_015 not in the Motif Atlas

Homologous match to J4_8C3A_022

Geometric discrepancy: 0.073

The information below is about J4_8C3A_022

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61885.4

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F-F-F

Number of instances in this motif group

5

Unit IDs

6ZMI|1|S2|A|671
6ZMI|1|S2|A|672
6ZMI|1|S2|G|673
*
6ZMI|1|S2|C|1032
6ZMI|1|S2|G|1033
6ZMI|1|S2|A|1034
6ZMI|1|S2|A|1035
6ZMI|1|S2|A|1036
6ZMI|1|S2|G|1037
*
6ZMI|1|S2|C|1078
6ZMI|1|S2|C|1079
6ZMI|1|S2|A|1080
6ZMI|1|S2|U|1081
6ZMI|1|S2|A|1082
6ZMI|1|S2|A|1083
6ZMI|1|S2|A|1084
6ZMI|1|S2|C|1085
6ZMI|1|S2|G|1086
6ZMI|1|S2|A|1087
6ZMI|1|S2|U|1088
6ZMI|1|S2|G|1089
*
6ZMI|1|S2|U|1160
6ZMI|1|S2|U|1161

Current chains

Chain S2

18S ribosomal RNA

Nearby chains

Chain L5

Large subunit ribosomal RNA; LSU rRNA

Chain Ln

60S ribosomal protein L41

Chain SL

40S ribosomal protein S11

Chain SN

40S ribosomal protein S13

Chain SO

40S ribosomal protein S14

Chain SW

40S ribosomal protein S15a

Chain SX

40S ribosomal protein S23

Chain Sa

40S ribosomal protein S26