SMTL ID : 7tql.1

CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Covalent)

GNP.1: 18 residues within 4Å: Chain A: V.40, D.41, T.42, G.43, K.44, T.45, K.46, E.60, G.63, I.64, T.65, D.128, N.156, K.157, D.159, R.160, A.225, H.226 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.40, A:D.41, A:T.42, A:G.43, A:K.44, A:K.44, A:T.45, A:T.45, A:T.65, A:N.156, A:K.157 Salt bridges: A:K.46, A:D.159 pi-Cation interactions: A:K.157, A:H.226

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-functional Binders)

5GP.2: 5 residues within 4Å: Chain B: C.1497, G.1498, C.1500 Chain C: C.33, A.34 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain 5: C.22, C.25, C.73, C.76 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:C.22, 5:C.73, 5:C.76 ZN.4: 4 residues within 4Å: Chain 8: C.19, C.22, C.37, C.40 3 PLIP interactions: 3 interactions with chain 8 Metal complexes: 8:C.19, 8:C.22, 8:C.40 ZN.5: 5 residues within 4Å: Chain 9: C.37, S.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:C.37, 9:C.42, 9:C.57, 9:C.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lapointe, C.P. et al., eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Nature (2022)

Release Date

2022-04-27

Peptides

Eukaryotic translation initiation factor 5B: A
Translation initiation factor eIF1A: D
ribosomal protein uS2: EF
40S ribosomal protein S2: G
40S ribosomal protein S4, X isoform: H
40S ribosomal protein S3: I
40S ribosomal protein S6: J
40S ribosomal protein S7: K
40S ribosomal protein S8: L
40S ribosomal protein S9: M
40S ribosomal protein S5: N
40S ribosomal protein S11: O
40S ribosomal protein S10: P
ribosomal protein uS15: Q
ribosomal protein eS12: R
ribosomal protein uS11: S
40S ribosomal protein S15: T
40S ribosomal protein S16: U
ribosomal protein eS17: V
ribosomal protein uS13: W
40S ribosomal protein S19: X
ribosomal protein uS10: Y
40S ribosomal protein S15a: Z
40S ribosomal protein S23: 0
Isoform 3 of 40S ribosomal protein S24: 1
40S ribosomal protein S21: 2
ribosomal protein eS25: 3
40S ribosomal protein S27: 4
40S ribosomal protein S26: 5
ribosomal protein eS28: 6
ribosomal protein eS30: 7
ribosomal protein uS14: 8
40S ribosomal protein S27a: 9
ribosomal protein eL41: a
Receptor of activated protein C kinase 1: b

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

D
4

E
B

F
C

G
D

H
E

I
F

J
G

K
H

L
I

M
J

N
K

O
L

P
M

Q
N

R
O

S
P

T
Q

U
R

V
S

W
T

X
U

Y
V

Z
W

0
X

1
Y

2
Z

3
a

4
b

5
c

6
d

7
e

8
f

9
g

a
h

b
j

Eukaryotic translation initiation factor 5B

Translation initiation factor eIF1A

ribosomal protein uS2

40S ribosomal protein S2

40S ribosomal protein S4, X isoform

40S ribosomal protein S3

40S ribosomal protein S6

40S ribosomal protein S7

40S ribosomal protein S8

40S ribosomal protein S9

40S ribosomal protein S5

40S ribosomal protein S11

40S ribosomal protein S10

ribosomal protein uS15

ribosomal protein eS12

ribosomal protein uS11

40S ribosomal protein S15

40S ribosomal protein S16

ribosomal protein eS17

ribosomal protein uS13

40S ribosomal protein S19

ribosomal protein uS10

40S ribosomal protein S15a

40S ribosomal protein S23

Isoform 3 of 40S ribosomal protein S24

40S ribosomal protein S21

ribosomal protein eS25

40S ribosomal protein S27

40S ribosomal protein S26

ribosomal protein eS28

ribosomal protein eS30

ribosomal protein uS14

40S ribosomal protein S27a

ribosomal protein eL41

Receptor of activated protein C kinase 1

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