SMTL ID : 7syv.1

Structure of the wt IRES eIF5B-containing pre-48S initiation complex, open conformation. Structure 14(wt)

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-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain F: C.22, N.24, C.25, C.73, C.76 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.22, F:C.25, F:C.73, F:C.76 ZN.2: 4 residues within 4Å: Chain P: C.153, C.158, C.173, C.176 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.153, P:C.158, P:C.173, P:C.176

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.3: 18 residues within 4Å: Chain X: H.46, V.47, D.48, T.49, G.50, K.51, T.52, K.53, G.70, T.72, N.163, K.164, D.166, R.167, A.232, H.233 Ligands: MG.4, NA.5 19 PLIP interactions: 19 interactions with chain X Hydrogen bonds: X:D.48, X:T.49, X:T.49, X:G.50, X:K.51, X:T.52, X:T.52, X:T.52, X:K.53, X:T.72, X:N.163, X:K.164, X:A.232, X:H.233 Salt bridges: X:K.51, X:K.51, X:K.51, X:D.166 pi-Stacking: X:H.233

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain X: T.52, T.72 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain X: G.70 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, Z.P. et al., Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. Embo J. (2022)

Release Date

2022-07-20

Peptides

40S ribosomal protein S24: B
Eukaryotic translation initiation factor 1A, X-chromosomal: C
40S ribosomal protein S25: D
40S ribosomal protein SA: E
eS26: F
eS1: G
eS27: H
40S ribosomal protein S2: I
eS28: J
uS3: K
eS29: L
40S ribosomal protein S4: M
eS30: N
uS7: O
40S ribosomal protein S27a: P
eS6: Q
RACK1: R
40S ribosomal protein S7: S
eS8: U
60s ribosomal protein l41: V
uS4: W
Eukaryotic translation initiation factor 5B: X
eS10: Y
uS17: 0
eS12: 1
uS15: 2
uS11: 3
uS19: 4
uS9: 5
eS17: 6
uS13: 7
eS19: 8
uS10: 9
40S ribosomal protein S21: a
uS8: b
uS12: c

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
Z

C
A

D
a

E
B

F
b

G
C

H
c

I
D

J
d

K
E

L
e

M
F

N
f

O
G

P
g

Q
H

R
h

S
I

U
J

V
n

W
K

X
x

Y
L

0
M

1
N

2
O

3
P

4
Q

5
R

6
S

7
T

8
U

9
V

a
W

b
X

c
Y

40S ribosomal protein S24

Eukaryotic translation initiation factor 1A, X-chromosomal

40S ribosomal protein S25

40S ribosomal protein SA

eS26

eS1

eS27

40S ribosomal protein S2

eS28

uS3

eS29

40S ribosomal protein S4

eS30

uS7

40S ribosomal protein S27a

eS6

RACK1

40S ribosomal protein S7

eS8

60s ribosomal protein l41

uS4

Eukaryotic translation initiation factor 5B

eS10

uS17

eS12

uS15

uS11

uS19

uS9

eS17

uS13

eS19

uS10

40S ribosomal protein S21

uS8

uS12

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