SMTL ID : 6yal.1

Mammalian 48S late-stage initiation complex with beta-globin mRNA

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-mer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.1: 11 residues within 4Å: Chain b: A.6, C.26, C.35, I.36, C.52, I.53, G.54, C.55, G.56, I.57, C.58 5 PLIP interactions: 5 interactions with chain b, Metal complexes: b:C.26, b:C.52, b:G.54, b:C.55, b:C.58 SF4.2: 7 residues within 4Å: Chain b: C.13, K.14, C.18, C.22, C.62, F.64, L.67 4 PLIP interactions: 4 interactions with chain b, Metal complexes: b:C.13, b:C.18, b:C.22, b:C.62

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Ligands: GNP.4 Chain b: S.114, Q.168, S.460 No protein-ligand interaction detected (PLIP)

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Covalent)(Non-covalent)

GNP.4: 15 residues within 4Å: Ligands: MG.3 Chain b: Y.84, F.89, T.108, N.109, G.110, I.111, G.112, K.113, S.114, T.115, Q.168, H.271, S.291, S.460 13 PLIP interactions: 13 interactions with chain b Hydrogen bonds: b:G.110, b:I.111, b:G.112, b:K.113, b:S.114, b:S.114, b:T.115, b:T.115, b:H.271, b:S.460 pi-Stacking: b:Y.84, b:Y.84 pi-Cation interactions: b:Y.84 GNP.5: 15 residues within 4Å: Chain b: R.209, D.213, L.214, S.215, G.217, E.218, M.354, E.356, F.357, N.378, G.379, G.381, K.382, T.383, H.517 14 PLIP interactions: 14 interactions with chain b Hydrogen bonds: b:R.209, b:R.209, b:S.215, b:S.215, b:G.217, b:G.379, b:G.381, b:K.382, b:T.383, b:T.383, b:T.383, b:T.384 Salt bridges: b:D.213, b:E.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simonetti, A. et al., Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep (2020)

Release Date

2020-04-08

Peptides

60s ribosomal protein ul41: B
40S ribosomal protein uS2: C
40S ribosomal protein eS1: D
40S ribosomal protein uS5: E
40S Ribosomal protein uS3: F
40S ribosomal protein eS4: G
40S Ribosomal protein uS7: H
40S ribosomal protein eS6: I
40S ribosomal protein eS7: J
40S ribosomal protein eS8: K
40S ribosomal protein uS4: L
40S ribosomal protein eS10: M
40S ribosomal protein uS17: N
40S ribosomal protein eS12: O
40S ribosomal protein uS15: P
40S ribosomal protein uS11: Q
40S ribosomal protein uS9: R
40S ribosomal protein eS17: S
40S ribosomal protein eS19: T
40S ribosomal protein uS10: U
40S ribosomal protein eS21: V
40S ribosomal protein uS8: W
40S ribosomal protein uS12: X
40S ribosomal protein eS24: Y
40S ribosomal protein eS26: Z
40S ribosomal protein eS27: 0
40S ribosomal protein eS28: 1
40S ribosomal protein uS14: 2
40S ribosomal protein eS31: 3
ribosomal protein RACK1: 4
40S ribosomal protein eS25: 5
40S ribosomal protein eS30: 6
Eukaryotic translation initiation factor 2 subunit alpha: 8
Eukaryotic translation initiation factor 2 subunit gamma: 9
eukaryotic translation initiation factor 1A: a
ATP-binding cassette sub-family E member 1 (ABCE1): b
40S ribosomal protein uS13: c
40S ribosomal protein uS19: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
l

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
S

S
T

T
V

U
W

V
X

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

4
g

5
n

6
i

8
A

9
B

a
j

b
k

c
U

d
R

60s ribosomal protein ul41

40S ribosomal protein uS2

40S ribosomal protein eS1

40S ribosomal protein uS5

40S Ribosomal protein uS3

40S ribosomal protein eS4

40S Ribosomal protein uS7

40S ribosomal protein eS6

40S ribosomal protein eS7

40S ribosomal protein eS8

40S ribosomal protein uS4

40S ribosomal protein eS10

40S ribosomal protein uS17

40S ribosomal protein eS12

40S ribosomal protein uS15

40S ribosomal protein uS11

40S ribosomal protein uS9

40S ribosomal protein eS17

40S ribosomal protein eS19

40S ribosomal protein uS10

40S ribosomal protein eS21

40S ribosomal protein uS8

40S ribosomal protein uS12

40S ribosomal protein eS24

40S ribosomal protein eS26

40S ribosomal protein eS27

40S ribosomal protein eS28

40S ribosomal protein uS14

40S ribosomal protein eS31

ribosomal protein RACK1

40S ribosomal protein eS25

40S ribosomal protein eS30

Eukaryotic translation initiation factor 2 subunit alpha

Eukaryotic translation initiation factor 2 subunit gamma

eukaryotic translation initiation factor 1A

ATP-binding cassette sub-family E member 1 (ABCE1)

40S ribosomal protein uS13

40S ribosomal protein uS19

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