SMTL ID : 7pnw.1

Mouse mitochondrial ribosome small subunit lacking m5U modification

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-mer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: C.493, A.930 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: A.787, A.788 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: G.66 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: G.228, A.230, A.231, A.232 Chain D: G.197 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: A.930, U.931 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: U.112, A.495, C.496 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: G.756 Chain K: K.59 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: A.257, C.258 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: U.26, A.179, U.180 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: C.419, A.431, G.940 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: C.407, G.441 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: C.413, A.416, U.438, A.439, U.440 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: U.494, A.495 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain A: U.226 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain A: A.657, A.658, A.659 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain A: U.7 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: A.800, G.801 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain A: A.45, C.46, C.167, A.168 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: A.153, C.158 Ligands: K.55 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain 0: Q.133 Chain A: C.58 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain A: U.287, A.288, A.289, A.290 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: U.350, G.351, U.352 No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain A: U.384, A.385, G.386 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: C.496, U.497, A.498 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain A: G.490, A.491 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: G.567, A.568, G.682, U.683 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain A: U.613, A.680, G.681, G.682 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain A: C.583, C.584, U.585, G.706 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: C.608, U.609, G.699 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain A: C.584 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain A: A.661, A.662 No protein-ligand interaction detected (PLIP) MG.34: 5 residues within 4Å: Chain A: U.917, A.918, A.919, G.923, G.924 No protein-ligand interaction detected (PLIP) MG.35: 7 residues within 4Å: Chain A: A.919, G.923, G.924, U.925, A.926, A.927 Ligands: K.60 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain A: A.451, A.453 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain A: C.607 Chain K: V.30, D.31 No protein-ligand interaction detected (PLIP) MG.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.39: 3 residues within 4Å: Chain A: A.731, A.732, A.733 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain A: G.830, C.831, G.949 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain A: G.948 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: A.376, G.377, A.453 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain A: C.170, G.172 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain A: U.797 Chain K: R.88 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain A: U.26, A.27 No protein-ligand interaction detected (PLIP) MG.46: 1 residues within 4Å: Chain A: C.432 No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain A: U.430 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain A: A.410 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: A.431, G.924, U.925 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain A: A.612, U.613, A.680, G.681 No protein-ligand interaction detected (PLIP) MG.51: 3 residues within 4Å: Chain A: U.70, A.71, A.72 No protein-ligand interaction detected (PLIP) MG.52: 1 residues within 4Å: Chain A: C.167 No protein-ligand interaction detected (PLIP) MG.53: 4 residues within 4Å: Chain A: U.621, C.622, U.624, A.674 No protein-ligand interaction detected (PLIP) MG.54: 4 residues within 4Å: Chain A: G.237, U.238, G.239, A.255 No protein-ligand interaction detected (PLIP) MG.65: 5 residues within 4Å: Chain B: H.90, D.221, D.237, D.238 Chain W: K.118 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.90, B:D.221, B:D.237, B:D.238 MG.70: 4 residues within 4Å: Chain X: K.127, T.128, S.304 Ligands: ATP.69 3 PLIP interactions: 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:T.128, H2O.29, H2O.29 MG.71: 3 residues within 4Å: Chain 3: R.136, M.139, N.140 No protein-ligand interaction detected (PLIP)

10 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.55: 5 residues within 4Å: Chain A: C.152, A.153, C.157, C.158 Ligands: MG.19 No protein-ligand interaction detected (PLIP) K.56: 5 residues within 4Å: Chain A: C.187, U.190, A.191, U.202, A.204 No protein-ligand interaction detected (PLIP) K.57: 4 residues within 4Å: Chain A: G.222, G.223, G.224, C.266 No protein-ligand interaction detected (PLIP) K.58: 5 residues within 4Å: Chain A: C.454, C.455, U.946, U.947, G.948 No protein-ligand interaction detected (PLIP) K.59: 5 residues within 4Å: Chain A: C.616, G.617, C.618, G.682, U.683 No protein-ligand interaction detected (PLIP) K.60: 5 residues within 4Å: Chain A: A.918, A.919, A.927, G.940 Ligands: MG.35 No protein-ligand interaction detected (PLIP) K.61: 5 residues within 4Å: Chain A: C.240, C.250, G.251 Chain J: P.73, N.74 No protein-ligand interaction detected (PLIP) K.62: 4 residues within 4Å: Chain A: C.920, A.921, A.926, A.927 No protein-ligand interaction detected (PLIP) K.63: 5 residues within 4Å: Chain A: G.5, U.6, G.15, G.16, C.17 No protein-ligand interaction detected (PLIP) K.64: 2 residues within 4Å: Chain A: G.699, A.700 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.66: 5 residues within 4Å: Chain O: C.92, C.103, C.106, C.141, Q.144 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.92, O:C.103, O:C.106, O:C.141

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.67: 10 residues within 4Å: Chain E: C.105, G.107, I.108 Chain P: K.65, C.66, C.69, E.70, C.101, K.103, K.104 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain E, Metal complexes: P:C.66, P:C.69, P:C.101, E:C.105 FES.68: 7 residues within 4Å: Chain M: G.25, C.26, R.29 Chain T: C.139, C.141, C.149, P.150 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain M, Metal complexes: T:C.139, T:C.141, T:C.149, M:C.26

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

ATP.69: 25 residues within 4Å: Chain X: H.60, P.77, R.79, Y.80, Q.83, C.91, L.92, M.93, R.95, E.122, K.123, G.124, T.125, G.126, K.127, T.128, L.129, S.304, T.306, Y.341, Y.353, P.381, E.382, E.385 Ligands: MG.70 20 PLIP interactions: 20 interactions with chain X Hydrogen bonds: X:Y.80, X:M.93, X:M.93, X:R.95, X:E.122, X:G.124, X:T.125, X:G.126, X:K.127, X:T.128, X:T.128, X:L.129, X:T.306, X:T.306, X:T.306, X:Y.341 Water bridges: X:K.127, X:S.302 Salt bridges: X:K.127, X:K.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itoh, Y. et al., Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Nature (2022)

Release Date

2022-06-15

Peptides

28S ribosomal protein S2, mitochondrial: B
28S ribosomal protein S24, mitochondrial: C
28S ribosomal protein S5, mitochondrial: D
28S ribosomal protein S6, mitochondrial: E
28S ribosomal protein S7, mitochondrial: F
28S ribosomal protein S9, mitochondrial: G
28S ribosomal protein S10, mitochondrial: H
28S ribosomal protein S11, mitochondrial: I
28S ribosomal protein S12, mitochondrial: J
28S ribosomal protein S14, mitochondrial: K
28S ribosomal protein S15, mitochondrial: L
28S ribosomal protein S16, mitochondrial: M
28S ribosomal protein S17, mitochondrial: N
28S ribosomal protein S18b, mitochondrial: O
28S ribosomal protein S18c, mitochondrial: P
28S ribosomal protein S21, mitochondrial: Q
28S ribosomal protein S22, mitochondrial: R
28S ribosomal protein S23, mitochondrial: S
28S ribosomal protein S25, mitochondrial: T
28S ribosomal protein S26, mitochondrial: U
28S ribosomal protein S27, mitochondrial: V
28S ribosomal protein S28, mitochondrial: W
28S ribosomal protein S29, mitochondrial: X
28S ribosomal protein S31, mitochondrial: Y
28S ribosomal protein S33, mitochondrial: Z
28S ribosomal protein S34, mitochondrial: 0
28S ribosomal protein S35, mitochondrial: 1
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1: 2
Aurora kinase A-interacting protein: 3
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 4

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

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
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
0

1
1

2
2

3
3

4
4

28S ribosomal protein S2, mitochondrial

28S ribosomal protein S24, mitochondrial

28S ribosomal protein S5, mitochondrial

28S ribosomal protein S6, mitochondrial

28S ribosomal protein S7, mitochondrial

28S ribosomal protein S9, mitochondrial

28S ribosomal protein S10, mitochondrial

28S ribosomal protein S11, mitochondrial

28S ribosomal protein S12, mitochondrial

28S ribosomal protein S14, mitochondrial

28S ribosomal protein S15, mitochondrial

28S ribosomal protein S16, mitochondrial

28S ribosomal protein S17, mitochondrial

28S ribosomal protein S18b, mitochondrial

28S ribosomal protein S18c, mitochondrial

28S ribosomal protein S21, mitochondrial

28S ribosomal protein S22, mitochondrial

28S ribosomal protein S23, mitochondrial

28S ribosomal protein S25, mitochondrial

28S ribosomal protein S26, mitochondrial

28S ribosomal protein S27, mitochondrial

28S ribosomal protein S28, mitochondrial

28S ribosomal protein S29, mitochondrial

28S ribosomal protein S31, mitochondrial

28S ribosomal protein S33, mitochondrial

28S ribosomal protein S34, mitochondrial

28S ribosomal protein S35, mitochondrial

Coiled-coil-helix-coiled-coil-helix domain-containing protein 1

Aurora kinase A-interacting protein

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

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