SMTL ID : 6zp4.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: C.23, C.26, C.74, C.77 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.23, D:C.26, D:C.74, D:C.77 ZN.2: 5 residues within 4Å: Chain 4: G.29, I.31, C.39, R.40 Chain R: G.1256 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:G.29 ZN.3: 5 residues within 4Å: Chain 5: C.121, E.125, C.126, C.141, C.144 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.121, 5:C.126, 5:C.141, 5:C.144 ZN.4: 6 residues within 4Å: Chain n: C.281, T.283, C.284, C.302, T.304, C.305 4 PLIP interactions: 4 interactions with chain n Metal complexes: n:T.283, n:C.284, n:C.302, n:C.305

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 18 residues within 4Å: Ligands: MG.6 Chain n: T.283, S.307 Chain p: H.49, V.50, A.51, H.52, G.53, K.54, S.55, T.56, V.57, I.77, T.78, D.134, K.191, A.226, Q.227 16 PLIP interactions: 14 interactions with chain p, 2 interactions with chain n Hydrogen bonds: p:H.49, p:A.51, p:H.52, p:G.53, p:K.54, p:S.55, p:T.56, p:V.57, p:T.78, p:T.78, p:C.135, p:A.226, p:A.226, n:S.307, n:S.307 Salt bridges: p:K.54

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Ligands: GTP.5 Chain p: S.55, T.78 2 PLIP interactions: 2 interactions with chain p Metal complexes: p:S.55, p:T.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoms, M. et al., Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science (2020)

Release Date

2020-07-29

Peptides

40S ribosomal protein SA: A
40S ribosomal protein S3a: B
40S ribosomal protein S2: C
40S ribosomal protein S26: D
40S ribosomal protein S4, X isoform: E
60S ribosomal protein L41: F
40S ribosomal protein S6: G
40S ribosomal protein S7: H
40S ribosomal protein S8: I
40S ribosomal protein S9: J
40S ribosomal protein S11: K
40S ribosomal protein S13: L
40S ribosomal protein S21: M
40S ribosomal protein S15a: N
40S ribosomal protein S24: O
40S ribosomal protein S27: P
40S ribosomal protein S30: Q
40S ribosomal protein S17: S
40S ribosomal protein S3: T
40S ribosomal protein S5: U
40S ribosomal protein S10: V
40S ribosomal protein S12: W
40S ribosomal protein S15: X
40S ribosomal protein S16: Y
40S ribosomal protein S18: Z
40S ribosomal protein S19: 0
40S ribosomal protein S20: 1
40S ribosomal protein S25: 2
40S ribosomal protein S28: 3
40S ribosomal protein S29: 4
Ubiquitin-40S ribosomal protein S27a: 5
Receptor of activated protein C kinase 1: 6
40S ribosomal protein S14: 7
40S ribosomal protein S23: 8
Eukaryotic translation initiation factor 1A, X-chromosomal: 9
Eukaryotic translation initiation factor 3 subunit I: a
Eukaryotic translation initiation factor 3 subunit B: b
Eukaryotic translation initiation factor 3 subunit A: c
Eukaryotic translation initiation factor 3 subunit C: d
Eukaryotic translation initiation factor 3 subunit E: e
Eukaryotic translation initiation factor 3 subunit F: f
Eukaryotic translation initiation factor 3 subunit H: g
Eukaryotic translation initiation factor 3 subunit K: h
Eukaryotic translation initiation factor 3 subunit L: i
Eukaryotic translation initiation factor 3 subunit M: j
Eukaryotic translation initiation factor 3 subunit D: k
Unknown factor: l
Eukaryotic translation initiation factor 2 subunit 2: n
Eukaryotic translation initiation factor 2 subunit 1: o
Eukaryotic translation initiation factor 2 subunit 3: p
Eukaryotic translation initiation factor 1: q
Non-structural protein 1: r

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
p

C
d

D
Q

E
q

F
W

G
r

H
s

I
t

J
c

K
n

L
m

M
y

N
D

O
z

P
R

Q
T

S
w

T
b

U
e

V
u

W
v

X
o

Y
g

Z
k

0
x

1
h

2
P

3
S

4
l

5
U

6
V

7
i

8
j

9
G

a
I

b
B

c
A

d
C

e
E

f
F

g
H

h
K

i
L

j
M

k
N

l
X

n
4

o
O

p
Y

q
Z

r
J

40S ribosomal protein SA

40S ribosomal protein S3a

40S ribosomal protein S2

40S ribosomal protein S26

40S ribosomal protein S4, X isoform

60S ribosomal protein L41

40S ribosomal protein S6

40S ribosomal protein S7

40S ribosomal protein S8

40S ribosomal protein S9

40S ribosomal protein S11

40S ribosomal protein S13

40S ribosomal protein S21

40S ribosomal protein S15a

40S ribosomal protein S24

40S ribosomal protein S27

40S ribosomal protein S30

40S ribosomal protein S17

40S ribosomal protein S3

40S ribosomal protein S5

40S ribosomal protein S10

40S ribosomal protein S12

40S ribosomal protein S15

40S ribosomal protein S16

40S ribosomal protein S18

40S ribosomal protein S19

40S ribosomal protein S20

40S ribosomal protein S25

40S ribosomal protein S28

40S ribosomal protein S29

Ubiquitin-40S ribosomal protein S27a

Receptor of activated protein C kinase 1

40S ribosomal protein S14

40S ribosomal protein S23

Eukaryotic translation initiation factor 1A, X-chromosomal

Eukaryotic translation initiation factor 3 subunit I

Eukaryotic translation initiation factor 3 subunit B

Eukaryotic translation initiation factor 3 subunit A

Eukaryotic translation initiation factor 3 subunit C

Eukaryotic translation initiation factor 3 subunit E

Eukaryotic translation initiation factor 3 subunit F

Eukaryotic translation initiation factor 3 subunit H

Eukaryotic translation initiation factor 3 subunit K

Eukaryotic translation initiation factor 3 subunit L

Eukaryotic translation initiation factor 3 subunit M

Eukaryotic translation initiation factor 3 subunit D

Unknown factor

Eukaryotic translation initiation factor 2 subunit 2

Eukaryotic translation initiation factor 2 subunit 1

Eukaryotic translation initiation factor 2 subunit 3

Eukaryotic translation initiation factor 1

Non-structural protein 1

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