SMTL ID : 9g5b.1

Assembly intermediate of human mitochondrial ribosome small subunit (State A)

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

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

MG.1: 1 residues within 4Å: Chain E: C.171 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain E: U.26, U.27, U.42, A.180, C.181 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain E: U.214, G.273 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain E: G.231, U.232, C.233, A.234, A.235 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain E: C.417, U.442, A.443, U.444 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain E: U.300, G.398 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain E: A.407 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: A.154, C.159 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: A.167, C.168, A.169 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain F: H.93, D.224, N.226, D.240, D.241 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.93, F:D.224, F:D.240, F:D.241 MG.17: 5 residues within 4Å: Chain 1: G.133, K.134, T.135, L.136 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:T.135

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain S: C.94, C.105, C.108, C.143, Q.146 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.94, S:C.105, S:C.108, S:C.143

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

FES.13: 8 residues within 4Å: Chain I: C.105, G.107, I.108 Chain T: C.65, C.68, C.100, K.102, K.103 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain I, Metal complexes: T:C.65, T:C.68, T:C.100, I:C.105 FES.14: 6 residues within 4Å: Chain Q: C.26, R.29 Chain X: C.139, C.141, C.149, P.150 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain Q, Metal complexes: X:C.139, X:C.141, X:C.149, Q:C.26

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

ATP.15: 22 residues within 4Å: Chain 1: P.84, F.87, Q.90, C.98, L.99, M.100, R.102, K.130, G.131, T.132, G.133, K.134, T.135, L.136, S.311, T.313, Y.348, Y.360, P.388, S.389, E.392 Ligands: MG.17 20 PLIP interactions: 20 interactions with chain 1 Hydrogen bonds: 1:F.87, 1:Q.90, 1:M.100, 1:M.100, 1:G.131, 1:T.132, 1:G.133, 1:K.134, 1:T.135, 1:T.135, 1:T.313, 1:T.313, 1:T.313, 1:Y.348, 1:S.389, 1:E.392 Salt bridges: 1:K.130, 1:K.134, 1:K.134 pi-Stacking: 1:Y.348

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.16: 11 residues within 4Å: Chain 1: Y.173, R.177, K.207, Y.208, V.209, D.238, G.241, I.242, H.291, N.292, K.295 12 PLIP interactions: 12 interactions with chain 1 Hydrogen bonds: 1:Y.173, 1:R.177, 1:V.209, 1:V.209, 1:V.209, 1:H.291, 1:N.292, 1:N.292 Salt bridges: 1:R.177, 1:D.238, 1:K.295, 1:K.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heinrichs, M. et al., Coupling of ribosome biogenesis and translation initiation in human mitochondria. Nat Commun (2025)

Release Date

2025-04-23

Peptides

28S ribosomal protein S34, mitochondrial: A
28S ribosomal protein S35, mitochondrial: B
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: C
Nitric oxide-associated protein 1: D
28S ribosomal protein S2, mitochondrial: F
28S ribosomal protein S24, mitochondrial: G
28S ribosomal protein S5, mitochondrial: H
28S ribosomal protein S6, mitochondrial: I
28S ribosomal protein S7, mitochondrial: J
28S ribosomal protein S9, mitochondrial: K
28S ribosomal protein S10, mitochondrial: L
28S ribosomal protein S11, mitochondrial: M
28S ribosomal protein S12, mitochondrial: N
28S ribosomal protein S14, mitochondrial: O
28S ribosomal protein S15, mitochondrial: P
28S ribosomal protein S16, mitochondrial: Q
28S ribosomal protein S17, mitochondrial: R
28S ribosomal protein S18b, mitochondrial: S
28S ribosomal protein S18c, mitochondrial: T
28S ribosomal protein S21, mitochondrial: U
28S ribosomal protein S22, mitochondrial: V
28S ribosomal protein S23, mitochondrial: W
28S ribosomal protein S25, mitochondrial: X
28S ribosomal protein S26, mitochondrial: Y
28S ribosomal protein S27, mitochondrial: Z
28S ribosomal protein S28, mitochondrial: 0
28S ribosomal protein S29, mitochondrial: 1
28S ribosomal protein S31, mitochondrial: 2
28S ribosomal protein S33, mitochondrial: 3
Putative ribosome-binding factor A, mitochondrial: 4
Dimethyladenosine transferase 1, mitochondrial: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
4

D
9

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

V
R

W
S

X
T

Y
U

Z
V

0
W

1
X

2
Y

3
Z

4
a

5
c

28S ribosomal protein S34, mitochondrial

28S ribosomal protein S35, mitochondrial

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

Nitric oxide-associated protein 1

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

Putative ribosome-binding factor A, mitochondrial

Dimethyladenosine transferase 1, mitochondrial

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