J4_6ZP4_003

3D structure

PDB id

6ZP4 (explore in PDB, NAKB, or RNA 3D Hub)

Description

SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2

Experimental method

ELECTRON MICROSCOPY

Resolution

2.9 Å

Loop

Sequence

AAG*CGAAAG*CCAUAAACGAUG*UU

Length

23 nucleotides

Bulged bases

6ZP4|1|2|A|672, 6ZP4|1|2|A|1083, 6ZP4|1|2|C|1085, 6ZP4|1|2|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_6ZP4_003 not in the Motif Atlas

Homologous match to J4_8C3A_022

Geometric discrepancy: 0.0726

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

6ZP4|1|2|A|671
6ZP4|1|2|A|672
6ZP4|1|2|G|673
*
6ZP4|1|2|C|1032
6ZP4|1|2|G|1033
6ZP4|1|2|A|1034
6ZP4|1|2|A|1035
6ZP4|1|2|A|1036
6ZP4|1|2|G|1037
*
6ZP4|1|2|C|1078
6ZP4|1|2|C|1079
6ZP4|1|2|A|1080
6ZP4|1|2|U|1081
6ZP4|1|2|A|1082
6ZP4|1|2|A|1083
6ZP4|1|2|A|1084
6ZP4|1|2|C|1085
6ZP4|1|2|G|1086
6ZP4|1|2|A|1087
6ZP4|1|2|U|1088
6ZP4|1|2|G|1089
*
6ZP4|1|2|U|1160
6ZP4|1|2|U|1161

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C

Eukaryotic translation initiation factor 3 subunit C

Chain D

40S ribosomal protein S15a

Chain Q

40S ribosomal protein S26

Chain W

60S ribosomal protein L41

Chain i

40S ribosomal protein S14

Chain j

40S ribosomal protein S23

Chain m

40S ribosomal protein S13

Chain n

40S ribosomal protein S11