SMTL ID : 7syx.1

Structure of the delta dII IRES eIF5B-containing 48S initiation complex, closed conformation. Structure 15(delta dII)

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

1 x ZN: ZINC ION(Non-covalent)

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Ligands: GTP.3 Chain b: V.47, D.48 No protein-ligand interaction detected (PLIP)

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

GTP.3: 20 residues within 4Å: Ligands: MG.2 Chain b: H.46, V.47, D.48, T.49, G.50, K.51, T.52, K.53, Q.64, G.70, I.71, T.72, P.111, G.112, H.113, K.164, R.167, A.232, H.233 21 PLIP interactions: 21 interactions with chain b Hydrogen bonds: b:T.49, b:T.49, b:G.50, b:K.51, b:T.52, b:T.52, b:Q.64, b:Q.64, b:T.72, b:T.72, b:T.72, b:H.113, b:R.167, b:A.232, b:H.233, b:H.233 Salt bridges: b:K.51, b:K.51, b:K.51 pi-Cation interactions: b:K.164, b:K.164

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

2022-07-13

Peptides

Eukaryotic translation initiation factor 1A, X-chromosomal: B
uS2: C
eS1: D
uS5: E
uS3: F
eS4: G
uS7: H
eS6: I
40S ribosomal protein S7: J
eS8: K
uS4: L
eS10: M
uS17: N
eS12: O
uS15: P
uS11: Q
uS19: R
uS9: S
eS17: T
uS13: U
eS19: V
uS10: W
eS21: X
uS8: Y
uS12: Z
40S ribosomal protein S24: 0
40S ribosomal protein S25: 1
eS26: 2
eS27: 3
eS28: 4
eS29: 5
eS30: 6
40S ribosomal protein S27a: 7
RACK1: 8
60s ribosomal protein l41: a
Eukaryotic translation initiation factor 5B: b

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
I

K
J

L
K

M
L

N
M

O
N

P
O

Q
P

R
Q

S
R

T
S

U
T

V
U

W
V

X
W

Y
X

Z
Y

0
Z

1
a

2
b

3
c

4
d

5
e

6
f

7
g

8
h

a
n

b
x

Eukaryotic translation initiation factor 1A, X-chromosomal

uS2

eS1

uS5

uS3

eS4

uS7

eS6

40S ribosomal protein S7

eS8

uS4

eS10

uS17

eS12

uS15

uS11

uS19

uS9

eS17

uS13

eS19

uS10

eS21

uS8

uS12

40S ribosomal protein S24

40S ribosomal protein S25

eS26

eS27

eS28

eS29

eS30

40S ribosomal protein S27a

RACK1

60s ribosomal protein l41

Eukaryotic translation initiation factor 5B

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