SMTL ID : 8cas.1

Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)

Coordinates
PDB Format
Method
ELECTRON MICROSCOPY
Oligo State
hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
Ligands
1 x A- A- A- A- U- G- U- C: mRNA(Non-covalent)
4 x ZN: ZINC ION(Non-covalent)
1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
5 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
1 x MET: METHIONINE(Non-covalent)
1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)
Links
RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP
Citation
Ikeuchi, K. et al., Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nat Commun (2023)
Release Date
2023-05-24
Peptides
40S ribosomal protein S0-A: A
40S ribosomal protein S1-A: B
40S ribosomal protein S2: C
40S ribosomal protein S4-B: D
40S ribosomal protein S6-B: E
40S ribosomal protein S8-A: F
40S ribosomal protein S9-A: G
40S ribosomal protein S11-A: H
40S ribosomal protein S13: I
40S ribosomal protein S14-A: J
40S ribosomal protein S21-A: K
40S ribosomal protein S22-A: L
40S ribosomal protein S23-A: M
40S ribosomal protein S24-A: N
40S ribosomal protein S26-A: O
40S ribosomal protein S27-A: P
40S ribosomal protein S30-A: Q
RPS15 isoform 1: R
40S ribosomal protein S3: S
40S ribosomal protein S10-A: T
40S ribosomal protein S12: U
40S ribosomal protein S16-A: V
40S ribosomal protein S17-A: W
40S ribosomal protein S18-A: X
40S ribosomal protein S19-A: Y
40S ribosomal protein S20: Z
40S ribosomal protein S25-A: 0
RPS29A isoform 1: 1
40S ribosomal protein S31: 2
Guanine nucleotide-binding protein subunit beta-like protein: 3
40S ribosomal protein S28-A: 4
Eukaryotic translation initiation factor 3 subunit I: 5
Eukaryotic translation initiation factor 3 subunit G: 6
TIF5 isoform 1: 8
Eukaryotic translation initiation factor 3 subunit A: 9
Eukaryotic translation initiation factor 3 subunit B: a
Eukaryotic translation initiation factor 3 subunit C: b
Eukaryotic translation initiation factor 4C: c
RLI1 isoform 1: d
40S ribosomal protein S5: f
60S ribosomal protein L40-A: g
60S ribosomal protein L41-A: h
SUI2 isoform 1: i
protein-synthesizing GTPase: j
SUI3 isoform 1: k
OTU domain-containing protein 2: l
40S ribosomal protein S7-A: m
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
P
B
Q
C
R
D
S
E
T
F
V
G
W
H
X
I
Y
J
Z
K
a
L
b
M
c
N
d
O
e
P
f
Q
g
R
E
S
B
T
D
U
F
V
H
W
I
X
J
Y
K
Z
L
0
M
1
N
2
O
3
h
4
i
5
l
6
r
8
m
9
o
a
p
b
q
c
A
d
k
f
C
g
y
h
n
i
j
j
G
k
s
l
x
m
U

40S ribosomal protein S0-A

40S ribosomal protein S1-A

40S ribosomal protein S2

40S ribosomal protein S4-B

40S ribosomal protein S6-B

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

RPS15 isoform 1

40S ribosomal protein S3

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

RPS29A isoform 1

40S ribosomal protein S31

Guanine nucleotide-binding protein subunit beta-like protein

40S ribosomal protein S28-A

Eukaryotic translation initiation factor 3 subunit I

Eukaryotic translation initiation factor 3 subunit G

TIF5 isoform 1

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 4C

RLI1 isoform 1

40S ribosomal protein S5

60S ribosomal protein L40-A

60S ribosomal protein L41-A

SUI2 isoform 1

protein-synthesizing GTPase

SUI3 isoform 1

OTU domain-containing protein 2

40S ribosomal protein S7-A

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