SMTL ID : 6zce.1

Structure of a yeast ABCE1-bound 43S pre-initiation complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain 6: C.24, S.26, C.39 Chain C: G.1433 No protein-ligand interaction detected (PLIP) ZN.2: 3 residues within 4Å: Chain 3: C.74, S.76, C.77 No protein-ligand interaction detected (PLIP) ZN.3: 3 residues within 4Å: Chain 4: C.56, C.59, T.61 No protein-ligand interaction detected (PLIP) ZN.4: 4 residues within 4Å: Chain 8: C.141, C.144, V.147, Y.148 1 PLIP interactions: 1 interactions with chain 8 Metal complexes: 8:V.147

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

ADP.5: 10 residues within 4Å: Ligands: MG.8 Chain h: G.110, T.111, N.112, G.113, I.114, G.115, K.116, S.117, S.299 6 PLIP interactions: 6 interactions with chain h Hydrogen bonds: h:G.113, h:I.114, h:G.115, h:K.116, h:S.117, h:S.299

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 1 residues within 4Å: Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.7: 15 residues within 4Å: Ligands: MG.6 Chain h: K.221, S.223, Q.363, G.364, G.385, E.386, N.387, G.388, T.389, G.390, K.391, T.392, T.393, S.546 7 PLIP interactions: 7 interactions with chain h Hydrogen bonds: h:G.364, h:G.388, h:G.388, h:T.389, h:K.391, h:T.392, h:S.546

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

SF4.9: 8 residues within 4Å: Chain h: C.29, C.55, I.56, G.57, C.58, G.59, I.60, C.61 0 PLIP interactions: SF4.10: 8 residues within 4Å: Chain h: 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

2020-10-07

Peptides

Eukaryotic translation initiation factor 3 subunit I: A
Eukaryotic translation initiation factor 3 subunit G: B
40S ribosomal protein S0-A: D
40S ribosomal protein S1-A: E
40S ribosomal protein S2: F
40S ribosomal protein S3: G
40S ribosomal protein S4-A: H
40S ribosomal protein S5: I
40S ribosomal protein S6-A: J
40S ribosomal protein S7-A: K
40S ribosomal protein S8-A: L
40S ribosomal protein S9-A: M
40S ribosomal protein S10-A: N
40S ribosomal protein S11-A: O
40S ribosomal protein S12: P
40S ribosomal protein S13: Q
40S ribosomal protein S14-A: R
40S ribosomal protein S15: S
40S ribosomal protein S16-A: T
40S ribosomal protein S17-A: U
40S ribosomal protein S18-A: V
40S ribosomal protein S19-A: W
40S ribosomal protein S20: X
40S ribosomal protein S21-A: Y
40S ribosomal protein S22-A: Z
40S ribosomal protein S23-A: 0
40S ribosomal protein S24-A: 1
40S ribosomal protein S25-A: 2
40S ribosomal protein S26-A: 3
40S ribosomal protein S27-A: 4
40S ribosomal protein S28-B: 5
40S ribosomal protein S29-A: 6
40S ribosomal protein S30-A: 7
Ubiquitin-40S ribosomal protein S31: 8
Guanine nucleotide-binding protein subunit beta-like protein: 9
Eukaryotic translation initiation factor 3 subunit A: a
Eukaryotic translation initiation factor 3 subunit B: b
Eukaryotic translation initiation factor 3 subunit C: c
Eukaryotic translation initiation factor 1A: d
Eukaryotic translation initiation factor eIF-1: e
Eukaryotic translation initiation factor 3 subunit J: fi
RNA recognition motif (unknown): g
Translation initiation factor RLI1: h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
l

B
r

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

O
M

P
N

Q
O

R
P

S
Q

T
R

U
S

V
T

W
U

X
V

Y
W

Z
X

0
Y

1
Z

2
a

3
b

4
c

5
d

6
e

7
f

8
g

9
h

a
o

b
p

c
q

d
i

e
m

f
t

i
s

g
j

h
k

Eukaryotic translation initiation factor 3 subunit I

Eukaryotic translation initiation factor 3 subunit G

40S ribosomal protein S0-A

40S ribosomal protein S1-A

40S ribosomal protein S2

40S ribosomal protein S3

40S ribosomal protein S4-A

40S ribosomal protein S5

40S ribosomal protein S6-A

40S ribosomal protein S7-A

40S ribosomal protein S8-A

40S ribosomal protein S9-A

40S ribosomal protein S10-A

40S ribosomal protein S11-A

40S ribosomal protein S12

40S ribosomal protein S13

40S ribosomal protein S14-A

40S ribosomal protein S15

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 S21-A

40S ribosomal protein S22-A

40S ribosomal protein S23-A

40S ribosomal protein S24-A

40S ribosomal protein S25-A

40S ribosomal protein S26-A

40S ribosomal protein S27-A

40S ribosomal protein S28-B

40S ribosomal protein S29-A

40S ribosomal protein S30-A

Ubiquitin-40S ribosomal protein S31

Guanine nucleotide-binding protein subunit beta-like protein

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

Eukaryotic translation initiation factor eIF-1

Eukaryotic translation initiation factor 3 subunit J

RNA recognition motif (unknown)

Translation initiation factor RLI1

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