SMTL ID : 6zu9.1

Structure of a yeast ABCE1-bound 48S initiation complex

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-mer

Ligands

1 x A- A- A- A- U- G- U- C: mRNA(Non-covalent)

A-A-A-A-U-G-U-C.1: 13 residues within 4Å: Chain A: G.1150, C.1637, G.1638, C.1639, C.1640, U.1761, G.1768, U.1769 Chain a: C.33, A.34, U.35, A.36 Chain f: K.67 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: C.449 Chain E: R.30, T.81 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:R.30 MG.3: 7 residues within 4Å: Chain A: C.1472, U.1473 Chain V: A.183, N.186, I.187, K.188, T.189 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:K.188 MG.8: 2 residues within 4Å: Ligands: ATP.9 Chain g: T.392 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain 4: C.21, C.24, C.39, C.42 No protein-ligand interaction detected (PLIP) ZN.5: 4 residues within 4Å: Chain 5: N.123, T.125, C.126, K.143 No protein-ligand interaction detected (PLIP) ZN.6: 4 residues within 4Å: Chain b: C.99, C.121, K.126, T.128 1 PLIP interactions: 1 interactions with chain b Metal complexes: b:K.126

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 10 residues within 4Å: Ligands: MG.10 Chain g: F.92, T.111, N.112, G.113, I.114, G.115, K.116, S.117, T.118 7 PLIP interactions: 7 interactions with chain g Hydrogen bonds: g:G.113, g:G.113, g:I.114, g:G.115, g:K.116, g:S.117, g:T.118

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.9: 14 residues within 4Å: Ligands: MG.8 Chain g: K.221, S.223, G.224, G.225, Y.251, E.386, N.387, G.388, T.389, G.390, K.391, T.392, S.546 7 PLIP interactions: 7 interactions with chain g Hydrogen bonds: g:G.224, g:G.225, g:Y.251, g:G.388, g:G.390, g:K.391, g:T.392

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.11: 8 residues within 4Å: Chain g: C.29, C.55, I.56, G.57, C.58, G.59, I.60, C.61 0 PLIP interactions: SF4.12: 8 residues within 4Å: Chain g: C.16, K.17, P.18, C.21, Q.23, E.24, C.25, A.48 0 PLIP interactions:

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kratzat, H. et al., A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Embo J. (2021)

Release Date

2020-10-28

Peptides

40S ribosomal protein S0-A: B
40S ribosomal protein S1-A: C
40S ribosomal protein S2: D
40S ribosomal protein S4-A: E
40S ribosomal protein S6-A: F
40S ribosomal protein S7-A: G
40S ribosomal protein S8-A: H
40S ribosomal protein S9-A: I
40S ribosomal protein S11-A: J
40S ribosomal protein S13: K
40S ribosomal protein S14-A: L
40S ribosomal protein S21-A: M
40S ribosomal protein S22-A: N
40S ribosomal protein S23-A: O
40S ribosomal protein S24-A: P
40S ribosomal protein S26-A: Q
40S ribosomal protein S27-A: R
40S ribosomal protein S30-A: S
40S ribosomal protein S15: T
40S ribosomal protein S3: U
Rps5p: V
40S ribosomal protein S10-A: W
40S ribosomal protein S12: X
40S ribosomal protein S16-A: Y
40S ribosomal protein S17-A: Z
40S ribosomal protein S18-A: 0
40S ribosomal protein S19-A: 1
40S ribosomal protein S20: 2
40S ribosomal protein S25-A: 3
40S ribosomal protein S29-A: 4
Ubiquitin-40S ribosomal protein S31: 5
Guanine nucleotide-binding protein subunit beta-like protein: 6
40S ribosomal protein S28-B: 7
Eukaryotic translation initiation factor 3 subunit I: 8
Eukaryotic translation initiation factor 3 subunit G: 9
Eukaryotic translation initiation factor 5: b
Eukaryotic translation initiation factor 3 subunit A: c
Eukaryotic translation initiation factor 3 subunit B: d
Eukaryotic translation initiation factor 3 subunit C: e
Eukaryotic translation initiation factor 1A: f
Translation initiation factor RLI1: g

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
P

C
Q

D
R

E
S

F
T

G
U

H
V

I
W

J
X

K
Y

L
Z

M
a

N
b

O
c

P
d

Q
e

R
f

S
g

T
E

U
B

V
C

W
D

X
F

Y
H

Z
I

0
J

1
K

2
L

3
M

4
N

5
O

6
h

7
i

8
l

9
r

b
m

c
o

d
p

e
q

f
A

g
k

40S ribosomal protein S0-A

40S ribosomal protein S1-A

40S ribosomal protein S2

40S ribosomal protein S4-A

40S ribosomal protein S6-A

40S ribosomal protein S7-A

40S ribosomal protein S8-A

40S ribosomal protein S9-A

40S ribosomal protein S11-A

40S ribosomal protein S13

40S ribosomal protein S14-A

40S ribosomal protein S21-A

40S ribosomal protein S22-A

40S ribosomal protein S23-A

40S ribosomal protein S24-A

40S ribosomal protein S26-A

40S ribosomal protein S27-A

40S ribosomal protein S30-A

40S ribosomal protein S15

40S ribosomal protein S3

Rps5p

40S ribosomal protein S10-A

40S ribosomal protein S12

40S ribosomal protein S16-A

40S ribosomal protein S17-A

40S ribosomal protein S18-A

40S ribosomal protein S19-A

40S ribosomal protein S20

40S ribosomal protein S25-A

40S ribosomal protein S29-A

Ubiquitin-40S ribosomal protein S31

Guanine nucleotide-binding protein subunit beta-like protein

40S ribosomal protein S28-B

Eukaryotic translation initiation factor 3 subunit I

Eukaryotic translation initiation factor 3 subunit G

Eukaryotic translation initiation factor 5

Eukaryotic translation initiation factor 3 subunit A

Eukaryotic translation initiation factor 3 subunit B

Eukaryotic translation initiation factor 3 subunit C

Eukaryotic translation initiation factor 1A

Translation initiation factor RLI1

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