SMTL ID : 8qsj.1

Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.110, E.112, C.113, C.123, C.126 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.110, A:C.113, A:C.123, A:C.126 ZN.2: 4 residues within 4Å: Chain E: C.76, C.79, C.92, H.98 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.76, E:C.79, E:C.92, E:H.98

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

MG.3: 2 residues within 4Å: Chain K: A.357, G.358 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain K: U.471, A.472, C.582, U.583 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain K: A.290, A.291, A.759, A.760 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain K: C.838, A.839 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain K: A.643, A.998 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain K: A.628, G.630 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain K: A.344 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain K: G.826 No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain K: A.798, A.799 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain K: G.1046, U.1392, G.1393, A.1394 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain K: A.270, G.271, A.301, G.303 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain K: A.803, C.804, U.805, U.1367 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain K: A.839, G.867, C.868 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain K: A.798, G.801, G.985 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain K: U.1061, G.1062, G.1063 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain K: A.1335, U.1336 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain K: A.638, A.639, U.1432 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain K: C.809, A.810 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain K: U.280, C.281 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain K: A.237, A.342 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain K: A.830, C.832, A.833 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain C: Q.54 Chain K: C.249 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain K: A.472, C.589 No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain O: G.124 No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain K: C.56, G.1063 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain K: A.197, A.623, A.624 No protein-ligand interaction detected (PLIP) MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain K: A.261, G.262 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain K: A.1546, A.1547, G.1548 Chain N: G.212 Chain W: H.11 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:H.11 MG.36: 3 residues within 4Å: Chain 4: S.46 Chain K: A.1160, A.1167 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain K: G.1022 Chain l: I.12, G.14 1 PLIP interactions: 1 interactions with chain l Metal complexes: l:G.14 MG.38: 5 residues within 4Å: Chain U: R.43, R.44, R.45, G.46, R.47 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:R.43, U:R.44 MG.39: 2 residues within 4Å: Chain K: G.224 Chain e: D.99 1 PLIP interactions: 1 interactions with chain e Metal complexes: e:D.99 MG.44: 3 residues within 4Å: Ligands: GNP.43 Chain v: S.157, T.183 2 PLIP interactions: 2 interactions with chain v Metal complexes: v:S.157, v:T.183

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.40: 5 residues within 4Å: Chain Q: C.64 Chain o: C.70, C.73, L.107, C.108 6 PLIP interactions: 5 interactions with chain o, 1 interactions with chain Q, Metal complexes: o:C.70, o:C.70, o:C.73, o:C.108, o:C.108, Q:C.64

1 x PM8: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE(Covalent)

PM8.41: 14 residues within 4Å: Chain r: R.6, E.38, F.39, N.42, Q.43, K.44, L.45, R.51, Q.54, K.57, G.58, F.61 Chain s: D.111, S.112 9 PLIP interactions: 8 interactions with chain r, 1 interactions with chain s Hydrophobic interactions: r:F.39, r:Q.43, r:F.61, r:F.61 Hydrogen bonds: r:N.42, r:K.44, r:R.51, s:S.112 Salt bridges: r:R.6

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.42: 17 residues within 4Å: Chain t: C.181, A.182, A.183, P.184, G.186, K.187, N.203, D.204, L.205, S.206, R.209, D.237, G.238, D.255, V.256, P.257, L.291 9 PLIP interactions: 9 interactions with chain t Hydrogen bonds: t:C.181, t:G.186, t:L.205, t:S.206, t:D.237, t:G.238, t:D.255 Salt bridges: t:K.187, t:D.255

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.43: 23 residues within 4Å: Ligands: MG.44 Chain v: N.83, K.84, D.86, N.112, C.113, V.114, P.152, N.153, V.154, G.155, K.156, S.157, S.158, V.176, G.177, G.178, E.179, P.180, G.181, I.182, T.183, G.205 22 PLIP interactions: 22 interactions with chain v Hydrogen bonds: v:N.83, v:K.84, v:K.84, v:N.112, v:C.113, v:V.114, v:N.153, v:V.154, v:G.155, v:K.156, v:K.156, v:S.157, v:S.158, v:G.177, v:G.177, v:G.181, v:I.182, v:T.183, v:T.183, v:G.205 Salt bridges: v:D.86 pi-Cation interactions: v:K.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T.G. et al., Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome. Nat Commun (2023)

Release Date

2023-12-13

Peptides

39S ribosomal protein L32, mitochondrial: A
39S ribosomal protein L33, mitochondrial: B
39S ribosomal protein L34, mitochondrial: C
39S ribosomal protein L35, mitochondrial: D
39S ribosomal protein L36, mitochondrial: E
39S ribosomal protein L37, mitochondrial: F
39S ribosomal protein L38, mitochondrial: G
39S ribosomal protein L39, mitochondrial: H
39S ribosomal protein L40, mitochondrial: I
39S ribosomal protein L41, mitochondrial: J
39S ribosomal protein L2, mitochondrial: M
39S ribosomal protein L3, mitochondrial: N
39S ribosomal protein L4, mitochondrial: O
39S ribosomal protein L9, mitochondrial: P
39S ribosomal protein L10, mitochondrial: Q
39S ribosomal protein L11, mitochondrial: R
39S ribosomal protein L13, mitochondrial: S
39S ribosomal protein L14, mitochondrial: T
39S ribosomal protein L15, mitochondrial: U
39S ribosomal protein L16, mitochondrial: V
39S ribosomal protein L17, mitochondrial: W
39S ribosomal protein L18, mitochondrial: X
39S ribosomal protein L19, mitochondrial: Y
39S ribosomal protein L20, mitochondrial: Z
39S ribosomal protein L21, mitochondrial: 0
39S ribosomal protein L22, mitochondrial: 1
39S ribosomal protein L23, mitochondrial: 2
39S ribosomal protein L24, mitochondrial: 3
39S ribosomal protein L27, mitochondrial: 4
39S ribosomal protein L28, mitochondrial: 5
39S ribosomal protein L47, mitochondrial: 6
39S ribosomal protein L30, mitochondrial: 7
39S ribosomal protein L42, mitochondrial: 8
Large ribosomal subunit protein mL43: 9
39S ribosomal protein L44, mitochondrial: a
39S ribosomal protein L45, mitochondrial: b
39S ribosomal protein L46, mitochondrial: c
39S ribosomal protein L48, mitochondrial: d
39S ribosomal protein L49, mitochondrial: e
39S ribosomal protein L50, mitochondrial: f
39S ribosomal protein L51, mitochondrial: g
39S ribosomal protein L52, mitochondrial: h
39S ribosomal protein L53, mitochondrial: i
39S ribosomal protein L54, mitochondrial: j
39S ribosomal protein L55, mitochondrial: k
Ribosomal protein 63, mitochondrial: l
Peptidyl-tRNA hydrolase ICT1, mitochondrial: m
Growth arrest and DNA damage-inducible proteins-interacting protein 1: n
39S ribosomal protein S18a, mitochondrial: o
39S ribosomal protein S30, mitochondrial: p
Mitochondrial assembly of ribosomal large subunit protein 1: q
MIEF1 upstream open reading frame protein: r
Acyl carrier protein, mitochondrial: s
5-methylcytosine rRNA methyltransferase NSUN4: t
Transcription termination factor 4, mitochondrial: u
Mitochondrial ribosome-associated GTPase 1: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
2

D
3

E
4

F
5

G
6

H
7

I
8

J
9

M
D

N
E

O
F

P
H

Q
I

R
J

S
K

T
L

U
M

V
N

W
O

X
P

Y
Q

Z
R

0
S

1
T

2
U

3
V

4
W

5
X

6
Y

7
Z

8
a

9
b

a
c

b
d

c
e

d
f

e
g

f
h

g
i

h
j

i
k

j
l

k
m

l
o

m
p

n
q

o
r

p
s

q
u

r
v

s
w

t
x

u
y

v
z

39S ribosomal protein L32, mitochondrial

39S ribosomal protein L33, mitochondrial

39S ribosomal protein L34, mitochondrial

39S ribosomal protein L35, mitochondrial

39S ribosomal protein L36, 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 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 L42, mitochondrial

Large ribosomal subunit protein mL43

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

Mitochondrial assembly of ribosomal large subunit protein 1

MIEF1 upstream open reading frame protein

Acyl carrier protein, mitochondrial

5-methylcytosine rRNA methyltransferase NSUN4

Transcription termination factor 4, mitochondrial

Mitochondrial ribosome-associated GTPase 1

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