SMTL ID : 9npy.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.10 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

21 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain G: T.31, I.33, V.36 Chain N: U.1631 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.31, G:I.33, G:V.36, H2O.10, H2O.29 MG.2: 3 residues within 4Å: Chain H: G.80, G.81 Chain N: A.1589 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:G.80, H2O.4, H2O.13, H2O.13, H2O.24 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain N: G.1226, G.1227 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain N: A.1258 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain N: C.1331, A.1489, G.1490, G.1491 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain N: G.1330, C.1331, A.1489, G.1490 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain N: U.1326, U.1496, G.1497 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain N: C.1518, U.1519 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain N: G.1327, G.1510, U.1511 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain N: C.1261, C.1262, U.1263, G.1517, C.1518 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain N: C.1261, C.1262 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain N: G.1604, G.1605 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain N: A.1259, A.1260 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain N: G.1385, G.1387 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain N: C.1216, U.1340 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain N: C.1216, A.1217, U.1643, C.1644 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain N: C.1219 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain N: U.1441, U.1442, C.1443 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain N: A.1386, G.1387 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain N: U.1602, G.1603, G.1605 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain K: C.121, C.126, C.141, C.144 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.121, K:C.126, K:C.141, K:C.144 ZN.4: 4 residues within 4Å: Chain M: C.21, C.24, C.39, C.42 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.21, M:C.24, M:C.39, M:C.42

9 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.5: 5 residues within 4Å: Chain M: N.26, H.28, C.39, Q.41 Chain N: G.1495 2 PLIP interactions: 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:H.28, H2O.18 K.25: 4 residues within 4Å: Chain N: U.1225, G.1226, G.1227, G.1638 No protein-ligand interaction detected (PLIP) K.26: 5 residues within 4Å: Chain N: G.1330, G.1335, C.1336, G.1491, U.1492 No protein-ligand interaction detected (PLIP) K.27: 6 residues within 4Å: Chain N: G.1328, U.1329, C.1493, U.1499, G.1500, C.1501 No protein-ligand interaction detected (PLIP) K.28: 3 residues within 4Å: Chain N: G.1255, G.1257, U.1494 No protein-ligand interaction detected (PLIP) K.29: 5 residues within 4Å: Chain N: G.1330, G.1334, G.1335, U.1496, A.1498 No protein-ligand interaction detected (PLIP) K.30: 4 residues within 4Å: Chain N: C.1341, U.1342, U.1343, A.1484 No protein-ligand interaction detected (PLIP) K.31: 3 residues within 4Å: Chain N: C.1493, U.1494, U.1499 No protein-ligand interaction detected (PLIP) K.32: 5 residues within 4Å: Chain N: C.1534, U.1535 Chain O: A.162, N.165, K.167 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:A.162, O:N.165, O:K.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gen, R. et al., SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals. Cell Rep (2025)

Release Date

2025-06-11

Peptides

40S ribosomal protein uS3, RPS3: A
40S ribosomal protein eS10, RPS10: B
40S ribosomal protein eS12, RPS12: C
40S ribosomal protein uS19, RPS15: D
40S ribosomal protein uS9, RPS16: E
40S ribosomal protein eS17, RPS17: F
40S ribosomal protein uS13, RPS18: G
40S ribosomal protein eS19, RPS19: H
40S ribosomal protein uS10, RPS20: I
40S ribosomal protein eS25, RPS25: J
40S ribosomal protein eS31, RPS27a: K
40S ribosomal protein eS28, RPS28: L
40S ribosomal protein uS14, RPS29: M
40S ribosomal protein uS7, RPS5: O
RACK1: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
J

C
L

D
O

E
Q

F
R

G
S

H
T

I
U

J
Y

K
b

L
c

M
d

O
E

P
g

40S ribosomal protein uS3, RPS3

40S ribosomal protein eS10, RPS10

40S ribosomal protein eS12, RPS12

40S ribosomal protein uS19, RPS15

40S ribosomal protein uS9, RPS16

40S ribosomal protein eS17, RPS17

40S ribosomal protein uS13, RPS18

40S ribosomal protein eS19, RPS19

40S ribosomal protein uS10, RPS20

40S ribosomal protein eS25, RPS25

40S ribosomal protein eS31, RPS27a

40S ribosomal protein eS28, RPS28

40S ribosomal protein uS14, RPS29

40S ribosomal protein uS7, RPS5

RACK1

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