SMTL ID : 7po4.1

Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-6-1-1-1-mer

Ligands

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

MG.1: 4 residues within 4Å: Chain A: G.106, U.108 Chain E: G.148, G.149 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: A.105, G.106, A.109 Ligands: K.34 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain 0: K.59 Chain A: A.247, G.248, G.311 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: U.340, G.341 Chain E: G.124 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: C.388, C.389, C.408, C.409 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: U.471, A.472, C.582, U.583 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: G.579, A.580 Chain P: R.65 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: A.356, A.357, G.358 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: A.618 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain A: A.197, G.622, A.623, A.624 Chain K: R.41 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: A.639, U.641, A.1431, U.1432 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: A.643, A.998 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: A.1002, U.1004 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: A.704, C.705 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain A: U.646, G.647, A.780, A.781, A.782 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain A: A.781, A.782 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain A: G.783 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: A.787, U.996 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain A: A.798, A.799 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: A.802, G.982, C.983 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: U.752, C.753 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain A: A.797, A.798, A.799, G.801, G.985 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain A: A.1204, A.1205, G.1206 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain A: U.988, C.989, U.990 No protein-ligand interaction detected (PLIP) MG.25: 6 residues within 4Å: Chain A: A.1547, A.1548, G.1549 Chain D: G.212, K.213 Chain M: H.11 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: M:H.11, D:G.212, H2O.24, H2O.31 MG.26: 5 residues within 4Å: Chain A: A.69, A.86, A.87, U.88 Chain F: R.69 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain A: G.778 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: U.702, A.703, G.751, U.752 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain A: G.1491, C.1492, G.1493 No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain A: U.177, U.187, G.188, G.348, G.349 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: U.184, A.185 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain A: A.803, C.804, U.805 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain B: A.35 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain d: D.99, I.100 6 PLIP interactions: 1 interactions with chain d, 5 Ligand-Water interactions Metal complexes: d:D.99, H2O.5, H2O.17, H2O.42, H2O.89, H2O.90

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

K.34: 5 residues within 4Å: Chain A: U.108, A.109, A.124, A.125 Ligands: MG.2 No protein-ligand interaction detected (PLIP) K.35: 4 residues within 4Å: Chain A: A.1044, A.1045, G.1046, A.1431 No protein-ligand interaction detected (PLIP) K.36: 4 residues within 4Å: Chain A: U.991, A.992, U.1484, A.1489 No protein-ligand interaction detected (PLIP) K.37: 4 residues within 4Å: Chain A: C.670, C.671, G.673, A.754 No protein-ligand interaction detected (PLIP) K.38: 5 residues within 4Å: Chain A: A.1510, U.1511, A.1512, A.1515, U.1516 No protein-ligand interaction detected (PLIP) K.39: 5 residues within 4Å: Chain 0: K.63 Chain A: A.247, G.248, G.311, G.312 No protein-ligand interaction detected (PLIP) K.40: 4 residues within 4Å: Chain A: U.1021, A.1023, A.1024, A.1026 No protein-ligand interaction detected (PLIP) K.43: 4 residues within 4Å: Chain 3: D.222, H.224 Chain N: F.48, T.49 3 PLIP interactions: 2 interactions with chain 3, 1 interactions with chain N Metal complexes: 3:D.222, 3:H.224, N:T.49

1 x ZN: ZINC ION(Non-covalent)

ZN.42: 6 residues within 4Å: Chain Y: C.110, E.112, C.113, C.123, Y.125, C.126 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.110, Y:C.113, Y:C.123, Y:C.126

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

FES.45: 9 residues within 4Å: Chain G: S.63, C.64 Chain n: Q.69, C.70, I.72, C.73, K.78, C.108, E.111 4 PLIP interactions: 3 interactions with chain n, 1 interactions with chain G, Metal complexes: n:C.70, n:C.73, n:C.108, G:C.64

1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)

8Q1.46: 32 residues within 4Å: Chain v: C.110, E.191, K.192, T.195, L.196 Chain w: A.2, P.3, R.6, V.9, L.10, L.12, L.16, T.26, F.30, Y.31, S.34, I.35, E.38, F.39, Q.43, K.44, E.46, R.51, Q.54, L.55, K.57, G.58, F.61, I.69 Chain x: M.105, S.112, L.113 17 PLIP interactions: 15 interactions with chain w, 2 interactions with chain v Hydrophobic interactions: w:P.3, w:V.9, w:T.26, w:F.30, w:Y.31, w:E.38, w:E.38, w:F.39, w:R.51, w:F.61, w:F.61, w:F.61, w:I.69, v:E.191, v:L.196 Hydrogen bonds: w:A.2 Salt bridges: w:R.6

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

39S ribosomal protein L2, mitochondrial: C
39S ribosomal protein L3, mitochondrial: D
39S ribosomal protein L4, mitochondrial: E
39S ribosomal protein L9, mitochondrial: F
39S ribosomal protein L10, mitochondrial: G
39S ribosomal protein L11, mitochondrial: H
39S ribosomal protein L13, mitochondrial: I
39S ribosomal protein L14, mitochondrial: J
39S ribosomal protein L15, mitochondrial: K
39S ribosomal protein L16, mitochondrial: L
39S ribosomal protein L17, mitochondrial: M
39S ribosomal protein L18, mitochondrial: N
39S ribosomal protein L19, mitochondrial: O
39S ribosomal protein L20, mitochondrial: P
39S ribosomal protein L21, mitochondrial: Q
39S ribosomal protein L22, mitochondrial: R
39S ribosomal protein L23, mitochondrial: S
39S ribosomal protein L24, mitochondrial: T
39S ribosomal protein L27, mitochondrial: U
39S ribosomal protein L28, mitochondrial: V
39S ribosomal protein L47, mitochondrial: W
39S ribosomal protein L30, mitochondrial: X
39S ribosomal protein L32, mitochondrial: Y
39S ribosomal protein L33, mitochondrial: Z
39S ribosomal protein L34, mitochondrial: 0
39S ribosomal protein L35, mitochondrial: 1
39S ribosomal protein L37, mitochondrial: 2
39S ribosomal protein L38, mitochondrial: 3
39S ribosomal protein L39, mitochondrial: 4
39S ribosomal protein L40, mitochondrial: 5
39S ribosomal protein L41, mitochondrial: 6
39S ribosomal protein L42, mitochondrial: 7
39S ribosomal protein L43, mitochondrial: 8
39S ribosomal protein L44, mitochondrial: 9
39S ribosomal protein L45, mitochondrial: a
39S ribosomal protein L46, mitochondrial: b
39S ribosomal protein L48, mitochondrial: c
39S ribosomal protein L49, mitochondrial: d
39S ribosomal protein L50, mitochondrial: e
39S ribosomal protein L51, mitochondrial: f
39S ribosomal protein L52, mitochondrial: g
39S ribosomal protein L53, mitochondrial: h
39S ribosomal protein L54, mitochondrial: i
39S ribosomal protein L55, mitochondrial: j
Ribosomal protein 63, mitochondrial: k
Peptidyl-tRNA hydrolase ICT1, mitochondrial: l
Growth arrest and DNA damage-inducible proteins-interacting protein 1: m
39S ribosomal protein S18a, mitochondrial: n
39S ribosomal protein S30, mitochondrial: o
39S ribosomal protein L12, mitochondrial: pqrstu
Mitochondrial assembly of ribosomal large subunit protein 1: v
MIEF1 upstream open reading frame protein: w
Acyl carrier protein, mitochondrial: x

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
W

V
X

W
Y

X
Z

Y
0

Z
1

0
2

1
3

2
5

3
6

4
7

5
8

6
9

7
a

8
b

9
c

a
d

b
e

c
f

d
g

e
h

f
i

g
j

h
k

i
l

j
m

k
o

l
p

m
q

n
r

o
s

p
t

q
u

r
v

s
w

t
x

u
y

v
za

w
zb

x
zc

39S ribosomal protein L2, mitochondrial

39S ribosomal protein L3, mitochondrial

39S ribosomal protein L4, mitochondrial

39S ribosomal protein L9, mitochondrial

39S ribosomal protein L10, mitochondrial

39S ribosomal protein L11, mitochondrial

39S ribosomal protein L13, mitochondrial

39S ribosomal protein L14, mitochondrial

39S ribosomal protein L15, mitochondrial

39S ribosomal protein L16, mitochondrial

39S ribosomal protein L17, mitochondrial

39S ribosomal protein L18, mitochondrial

39S ribosomal protein L19, mitochondrial

39S ribosomal protein L20, mitochondrial

39S ribosomal protein L21, mitochondrial

39S ribosomal protein L22, mitochondrial

39S ribosomal protein L23, mitochondrial

39S ribosomal protein L24, mitochondrial

39S ribosomal protein L27, mitochondrial

39S ribosomal protein L28, mitochondrial

39S ribosomal protein L47, mitochondrial

39S ribosomal protein L30, mitochondrial

39S ribosomal protein L32, mitochondrial

39S ribosomal protein L33, mitochondrial

39S ribosomal protein L34, mitochondrial

39S ribosomal protein L35, mitochondrial

39S ribosomal protein L37, mitochondrial

39S ribosomal protein L38, mitochondrial

39S ribosomal protein L39, mitochondrial

39S ribosomal protein L40, mitochondrial

39S ribosomal protein L41, mitochondrial

39S ribosomal protein L42, mitochondrial

39S ribosomal protein L43, mitochondrial

39S ribosomal protein L44, mitochondrial

39S ribosomal protein L45, mitochondrial

39S ribosomal protein L46, mitochondrial

39S ribosomal protein L48, mitochondrial

39S ribosomal protein L49, mitochondrial

39S ribosomal protein L50, mitochondrial

39S ribosomal protein L51, mitochondrial

39S ribosomal protein L52, mitochondrial

39S ribosomal protein L53, mitochondrial

39S ribosomal protein L54, mitochondrial

39S ribosomal protein L55, mitochondrial

Ribosomal protein 63, mitochondrial

Peptidyl-tRNA hydrolase ICT1, mitochondrial

Growth arrest and DNA damage-inducible proteins-interacting protein 1

39S ribosomal protein S18a, mitochondrial

39S ribosomal protein S30, mitochondrial

39S ribosomal protein L12, mitochondrial

Mitochondrial assembly of ribosomal large subunit protein 1

MIEF1 upstream open reading frame protein

Acyl carrier protein, mitochondrial

Related Entries With Identical Sequence