SMTL ID : 8cbj.1

Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis 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-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.37, C.40, C.56, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.37, A:C.40, A:C.56, A:C.59 ZN.2: 5 residues within 4Å: Chain C: C.21, C.24, S.26, C.39, C.42 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.21, C:C.24, C:C.39, C:C.42

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

MG.3: 3 residues within 4Å: Chain b: A.619, A.620, A.621 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain b: A.62, U.82 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain b: G.95 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain b: A.387, A.401 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain b: G.549, A.550 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain b: G.95, C.402, G.403 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain b: G.91, A.93, G.398 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain b: G.1035 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain b: G.624, A.1025 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain b: C.424, C.427, G.429 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain b: G.634, A.635, A.636, A.807 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain b: C.49, A.425 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain b: G.386, C.402 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain b: G.377, A.378, U.379 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain b: G.42, U.98 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain b: A.970, A.971 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain b: A.862, A.863, G.866 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain b: C.627, U.968 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain b: G.16, U.608, C.614 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain b: C.424, G.426 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain b: G.371, A.605, G.607 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain b: A.622, A.623, C.1028, U.1031 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain b: G.1685 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain b: A.460, G.461 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain b: U.608 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain b: G.552, G.553, C.554, A.556 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain b: A.19 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain b: G.383 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain b: A.100, C.361 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain b: G.552, A.555, A.556 No protein-ligand interaction detected (PLIP) MG.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain b: A.341 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain b: G.457, G.458 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain b: G.1109, G.1110 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain b: A.753, A.754 No protein-ligand interaction detected (PLIP) MG.39: 3 residues within 4Å: Chain b: G.523, U.524, A.527 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain b: G.1294 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain b: A.100, U.101, C.361 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain b: A.43, U.44, A.46, A.47 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain b: A.470 No protein-ligand interaction detected (PLIP) MG.44: 3 residues within 4Å: Chain b: A.622, A.623, C.625 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain b: U.144, U.1684 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain O: R.221 Chain b: A.752, A.753 No protein-ligand interaction detected (PLIP) MG.47: 3 residues within 4Å: Chain b: U.618, A.619, A.1030 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain b: U.122 No protein-ligand interaction detected (PLIP)

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 S27-A: A
40S ribosomal protein S28-A: B
RPS29A isoform 1: C
40S ribosomal protein S30-A: D
Guanine nucleotide-binding protein subunit beta-like protein: E
Pre-rRNA-processing protein PNO1: F
ENP1 isoform 1: G
LTV1 isoform 1: H
TSR1 isoform 1: I
non-specific serine/threonine protein kinase: J
40S ribosomal protein S0-A: K
40S ribosomal protein S1-A: L
40S ribosomal protein S2: M
40S ribosomal protein S3: N
40S ribosomal protein S4-B: O
40S ribosomal protein S5: P
40S ribosomal protein S6-B: Q
40S ribosomal protein S7-A: R
40S ribosomal protein S8-A: S
40S ribosomal protein S9-A: T
40S ribosomal protein S11-A: U
40S ribosomal protein S12: V
40S ribosomal protein S13: W
40S ribosomal protein S14-A: X
RPS15 isoform 1: Y
40S ribosomal protein S16-A: Z
40S ribosomal protein S17-A: 0
40S ribosomal protein S18-A: 1
40S ribosomal protein S19-A: 2
40S ribosomal protein S20: 3
40S ribosomal protein S21-A: 4
40S ribosomal protein S22-A: 5
40S ribosomal protein S23-A: 6
40S ribosomal protein S24-A: 7
40S ribosomal protein S25-A: 8
20S-pre-rRNA D-site endonuclease NOB1: 9
rRNA adenine N(6)-methyltransferase: a
OTU domain-containing protein 2: c

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
b

B
c

C
d

D
e

E
g

F
h

G
i

H
j

I
k

J
l

K
A

L
B

M
C

N
D

O
E

P
F

Q
G

R
H

S
I

T
J

U
L

V
M

W
N

X
O

Y
P

Z
Q

0
R

1
S

2
T

3
U

4
V

5
W

6
X

7
Y

8
Z

9
a

a
y

c
K

40S ribosomal protein S27-A

40S ribosomal protein S28-A

RPS29A isoform 1

40S ribosomal protein S30-A

Guanine nucleotide-binding protein subunit beta-like protein

Pre-rRNA-processing protein PNO1

ENP1 isoform 1

LTV1 isoform 1

TSR1 isoform 1

non-specific serine/threonine protein kinase

40S ribosomal protein S0-A

40S ribosomal protein S1-A

40S ribosomal protein S2

40S ribosomal protein S3

40S ribosomal protein S4-B

40S ribosomal protein S5

40S ribosomal protein S6-B

40S ribosomal protein S7-A

40S ribosomal protein S8-A

40S ribosomal protein S9-A

40S ribosomal protein S11-A

40S ribosomal protein S12

40S ribosomal protein S13

40S ribosomal protein S14-A

RPS15 isoform 1

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

20S-pre-rRNA D-site endonuclease NOB1

rRNA adenine N(6)-methyltransferase

OTU domain-containing protein 2

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