SMTL ID : 7pnt.1

Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA and Tfb1m

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-mer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: A.787, A.788 Chain G: R.383 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: C.65, G.66 No protein-ligand interaction detected (PLIP) MG.3: 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.4: 3 residues within 4Å: Chain A: U.112, A.495, C.496 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: G.756 Chain K: K.59 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: C.258 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: U.26, A.179, U.180 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain A: C.413, A.416, U.438, A.439, U.440 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: A.658, A.659 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: C.580, A.800, G.801 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: A.45, C.46, C.167, A.168 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain A: A.153, C.158 Ligands: K.33 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain A: A.288, A.289, A.290 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain A: U.384, A.385 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain A: A.498, C.506 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: G.567, A.568, U.683 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain A: C.583, C.584, U.585, G.706 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: C.588, U.609, G.699 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain A: C.584, G.704 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain A: A.662 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain A: A.197 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain A: G.377, A.451, A.453, C.945, U.946 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: C.167, C.170 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: U.797 Chain K: I.87, R.88 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain A: A.27 Ligands: K.39 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain A: U.70, A.71 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain A: G.169 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain A: G.237, U.238, G.239, A.255 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: U.360, A.361 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain A: U.698, G.699 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain A: G.186 No protein-ligand interaction detected (PLIP) MG.40: 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.45: 4 residues within 4Å: Chain X: K.127, T.128, S.304 Ligands: ATP.44 3 PLIP interactions: 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:T.128, H2O.17, H2O.17

7 x K: POTASSIUM ION(Non-functional Binders)

K.33: 5 residues within 4Å: Chain A: C.152, A.153, C.157, C.158 Ligands: MG.12 No protein-ligand interaction detected (PLIP) K.34: 6 residues within 4Å: Chain A: C.187, A.189, U.190, A.191, U.202, A.204 No protein-ligand interaction detected (PLIP) K.35: 4 residues within 4Å: Chain A: G.222, G.223, G.224, C.266 No protein-ligand interaction detected (PLIP) K.36: 6 residues within 4Å: Chain A: A.612, C.616, G.617, C.618, G.682, U.683 No protein-ligand interaction detected (PLIP) K.37: 5 residues within 4Å: Chain A: G.5, U.6, G.15, G.16, C.17 No protein-ligand interaction detected (PLIP) K.38: 2 residues within 4Å: Chain A: G.422, G.423 No protein-ligand interaction detected (PLIP) K.39: 4 residues within 4Å: Chain A: A.27, A.28, U.29 Ligands: MG.26 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.41: 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.42: 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.43: 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: 1 interactions with chain M, 3 interactions with chain T, Metal complexes: M:C.26, T:C.139, T:C.141, T:C.149

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

ATP.44: 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.45 18 PLIP interactions: 18 interactions with chain X Hydrogen bonds: X:Y.80, X:Q.83, X:M.93, X:M.93, X:R.95, X:G.124, X:T.125, X:G.126, X:K.127, X:T.128, X:L.129, X:T.306, X:T.306, X:T.306, X:Y.341 Water bridges: 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
Aurora kinase A-interacting protein: 2
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 3
Putative ribosome-binding factor A, mitochondrial: 4
Dimethyladenosine transferase 1, mitochondrial: 5

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
3

3
4

4
a

5
c

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

Aurora kinase A-interacting protein

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

Putative ribosome-binding factor A, mitochondrial

Dimethyladenosine transferase 1, mitochondrial

Related Entries With Identical Sequence