SMTL ID : 9hcd.1

Mouse mitoribosome large subunit assembly intermediate (with uL16m) bound to MRM3-dimer, DDX28 and the MALSU-L0R8F8-mt-ACP complex, state A2 (SAMC knock-out)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain X: C.109, E.111, C.112, C.122, Y.124, C.125 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.109, X:C.112, X:C.122, X:C.125

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

FES.2: 9 residues within 4Å: Chain G: R.63, C.64 Chain i: Q.69, C.70, I.72, C.73, K.78, C.108, E.111 5 PLIP interactions: 3 interactions with chain i, 2 interactions with chain G, Metal complexes: i:C.70, i:C.70, i:C.108, G:C.64, G:C.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glasgow, R. et al., The mitochondrial methylation potential gates early and late ribosome assembly. Nat Commun (2025)

Release Date

2025-06-11

Peptides

Large ribosomal subunit protein uL2m: C
Large ribosomal subunit protein uL3m: D
Large ribosomal subunit protein uL4m: E
Large ribosomal subunit protein bL9m: F
Large ribosomal subunit protein uL10m: G
Large ribosomal subunit protein uL11m: H
Large ribosomal subunit protein uL13m: I
Large ribosomal subunit protein uL14m: J
Large ribosomal subunit protein uL15m: K
Large ribosomal subunit protein uL16m: L
Large ribosomal subunit protein bL17m: M
Large ribosomal subunit protein uL18m: N
Large ribosomal subunit protein bL19m: O
Large ribosomal subunit protein bL20m: P
Large ribosomal subunit protein bL21m: Q
Large ribosomal subunit protein uL22m: R
Large ribosomal subunit protein uL23m: S
Large ribosomal subunit protein uL24m: T
Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32m: U
Large ribosomal subunit protein uL29m: V
Large ribosomal subunit protein uL30m: W
Large ribosomal subunit protein bL32m: X
Large ribosomal subunit protein mL37: Y
Large ribosomal subunit protein mL38: Z
Large ribosomal subunit protein mL39: 0
Large ribosomal subunit protein mL40: 1
Large ribosomal subunit protein mL41: 2
Large ribosomal subunit protein mL42: 3
Large ribosomal subunit protein mL43: 4
Large ribosomal subunit protein mL44: 5
Large ribosomal subunit protein mL45: 6
Large ribosomal subunit protein mL46: 7
Large ribosomal subunit protein mL48: 8
Large ribosomal subunit protein mL49: 9
Large ribosomal subunit protein mL50: a
Large ribosomal subunit protein mL51: b
Large ribosomal subunit protein mL52: c
Large ribosomal subunit protein mL53: d
Large ribosomal subunit protein mL54: e
Large ribosomal subunit protein mL63: f
Large ribosomal subunit protein mL62: g
Large ribosomal subunit protein mL64: h
Large ribosomal subunit protein mL66: i
Large ribosomal subunit protein mL65: j
Mitochondrial assembly of ribosomal large subunit protein 1: k
Predicted gene, 55359: l
Acyl carrier protein, mitochondrial: m
rRNA methyltransferase 3, mitochondrial: no
Probable ATP-dependent RNA helicase DDX28: p

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
D

D
E

E
F

F
H

G
I

H
J

I
K

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

T
V

U
X

V
Y

W
Z

X
0

Y
5

Z
6

0
7

1
8

2
9

3
a

4
b

5
c

6
d

7
e

8
f

9
g

a
h

b
i

c
j

d
k

e
l

f
o

g
p

h
q

i
r

j
s

k
u

l
v

m
w

n
x

o
y

p
z

Large ribosomal subunit protein uL2m

Large ribosomal subunit protein uL3m

Large ribosomal subunit protein uL4m

Large ribosomal subunit protein bL9m

Large ribosomal subunit protein uL10m

Large ribosomal subunit protein uL11m

Large ribosomal subunit protein uL13m

Large ribosomal subunit protein uL14m

Large ribosomal subunit protein uL15m

Large ribosomal subunit protein uL16m

Large ribosomal subunit protein bL17m

Large ribosomal subunit protein uL18m

Large ribosomal subunit protein bL19m

Large ribosomal subunit protein bL20m

Large ribosomal subunit protein bL21m

Large ribosomal subunit protein uL22m

Large ribosomal subunit protein uL23m

Large ribosomal subunit protein uL24m

Large ribosomal subunit protein bL28m,Large ribosomal subunit protein bL32m

Large ribosomal subunit protein uL29m

Large ribosomal subunit protein uL30m

Large ribosomal subunit protein bL32m

Large ribosomal subunit protein mL37

Large ribosomal subunit protein mL38

Large ribosomal subunit protein mL39

Large ribosomal subunit protein mL40

Large ribosomal subunit protein mL41

Large ribosomal subunit protein mL42

Large ribosomal subunit protein mL43

Large ribosomal subunit protein mL44

Large ribosomal subunit protein mL45

Large ribosomal subunit protein mL46

Large ribosomal subunit protein mL48

Large ribosomal subunit protein mL49

Large ribosomal subunit protein mL50

Large ribosomal subunit protein mL51

Large ribosomal subunit protein mL52

Large ribosomal subunit protein mL53

Large ribosomal subunit protein mL54

Large ribosomal subunit protein mL63

Large ribosomal subunit protein mL62

Large ribosomal subunit protein mL64

Large ribosomal subunit protein mL66

Large ribosomal subunit protein mL65

Mitochondrial assembly of ribosomal large subunit protein 1

Predicted gene, 55359

Acyl carrier protein, mitochondrial

rRNA methyltransferase 3, mitochondrial

Probable ATP-dependent RNA helicase DDX28

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