SMTL ID : 6ft6.1

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors

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-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain J: C.51, C.54, H.67, H.73 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.51, J:C.54, J:H.67 ZN.4: 4 residues within 4Å: Chain 9: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 9 Metal complexes: 9:C.19, 9:C.22, 9:C.34, 9:C.37 ZN.7: 5 residues within 4Å: Chain e: C.39, C.42, C.57, C.59, C.60 3 PLIP interactions: 3 interactions with chain e Metal complexes: e:C.39, e:C.42, e:C.57 ZN.8: 3 residues within 4Å: Chain h: K.35, C.36, W.51 1 PLIP interactions: 1 interactions with chain h Metal complexes: h:C.36

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 22 residues within 4Å: Chain 1: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, V.194, Q.195, A.198, T.200, T.201, T.221, P.222, N.288, K.289, D.291, S.321, C.322, Q.323 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain 1 Hydrogen bonds: 1:Y.175, 1:N.177, 1:V.178, 1:G.179, 1:K.180, 1:S.181, 1:S.181, 1:S.182, 1:V.194, 1:A.198, 1:T.201, 1:T.201, 1:T.201, 1:N.288, 1:K.289, 1:C.322, 1:Q.323, 1:Q.323, 1:Q.323 Salt bridges: 1:K.180, 1:K.180, 1:D.291 GTP.5: 19 residues within 4Å: Ligands: MG.6 Chain c: K.261, L.264, H.287, A.288, P.324, N.325, T.326, G.327, K.328, S.329, S.330, V.343, A.344, P.345, P.347, E.349, T.350 Chain n: U.2318 19 PLIP interactions: 19 interactions with chain c Hydrogen bonds: c:K.261, c:K.261, c:H.287, c:A.288, c:T.326, c:G.327, c:K.328, c:S.329, c:S.329, c:S.329, c:S.330, c:S.330, c:A.344, c:A.344, c:E.349, c:T.350, c:T.350 Salt bridges: c:K.328, c:K.328

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain 1: Y.197, A.198, F.199, T.200, T.201 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain 1 Metal complexes: 1:A.198, 1:T.200 MG.6: 5 residues within 4Å: Ligands: GTP.5 Chain c: P.324, N.325, T.326, P.347 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schuller, J.M. et al., Structure of the nuclear exosome captured on a maturing preribosome. Science (2018)

Release Date

2018-03-28

Peptides

60S ribosomal protein L2-A: B
60S ribosomal protein L3: C
60S ribosomal protein L4-A: D
60S ribosomal protein L5: E
60S ribosomal protein L6-A: F
60S ribosomal protein L7-A: G
60S ribosomal protein L8-A: H
60S ribosomal protein L9-A: I
Bud site selection protein 20: J
60S ribosomal protein L11-A: K
60S ribosomal protein L13-A: L
60S ribosomal protein L14-A: M
60S ribosomal protein L15-A: N
60S ribosomal protein L16-A: O
60S ribosomal protein L17-A: P
60S ribosomal protein L18-A: Q
60S ribosomal protein L19-A: R
60S ribosomal protein L20-A: S
60S ribosomal protein L21-A: T
60S ribosomal protein L22-A: U
60S ribosomal protein L23-A: V
Ribosome assembly factor MRT4: W
60S ribosomal protein L25: X
60S ribosomal protein L26-A: Y
60S ribosomal protein L27-A: Z
60S ribosomal protein L28: 0
Nucleolar GTP-binding protein 1: 1
60S ribosomal protein L30: 2
60S ribosomal protein L31-A: 3
60S ribosomal protein L32: 4
60S ribosomal protein L33-A: 5
60S ribosomal protein L34-A: 6
60S ribosomal protein L35-A: 7
60S ribosomal protein L36-A: 8
60S ribosomal protein L37-A: 9
60S ribosomal protein L38: a
60S ribosomal protein L39: b
Nucleolar GTP-binding protein 2: c
Pescadillo homolog: d
60S ribosomal protein L43-A: e
Ribosome biogenesis protein NSA2: f
Nuclear GTP-binding protein NUG1: g
Ribosome biogenesis protein RLP24: h
Ribosome biogenesis protein RPF2: i
Regulator of ribosome biosynthesis: j
Ribosome assembly protein 4: k
Eukaryotic translation initiation factor 6: l
UPF0642 protein YBL028C: m
Probable metalloprotease ARX1: p
rRNA-processing protein CGR1: q
Exosome complex exonuclease RRP6: r
Exosome complex protein LRP1: s
ATP-dependent RNA helicase DOB1: t
MPP6: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
I

K
J

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
a

1
b

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
p

f
r

g
s

h
u

i
v

j
w

k
x

l
y

m
z

p
4

q
5

r
KK

s
LL

t
MM

u
NN

60S ribosomal protein L2-A

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L5

60S ribosomal protein L6-A

60S ribosomal protein L7-A

60S ribosomal protein L8-A

60S ribosomal protein L9-A

Bud site selection protein 20

60S ribosomal protein L11-A

60S ribosomal protein L13-A

60S ribosomal protein L14-A

60S ribosomal protein L15-A

60S ribosomal protein L16-A

60S ribosomal protein L17-A

60S ribosomal protein L18-A

60S ribosomal protein L19-A

60S ribosomal protein L20-A

60S ribosomal protein L21-A

60S ribosomal protein L22-A

60S ribosomal protein L23-A

Ribosome assembly factor MRT4

60S ribosomal protein L25

60S ribosomal protein L26-A

60S ribosomal protein L27-A

60S ribosomal protein L28

Nucleolar GTP-binding protein 1

60S ribosomal protein L30

60S ribosomal protein L31-A

60S ribosomal protein L32

60S ribosomal protein L33-A

60S ribosomal protein L34-A

60S ribosomal protein L35-A

60S ribosomal protein L36-A

60S ribosomal protein L37-A

60S ribosomal protein L38

60S ribosomal protein L39

Nucleolar GTP-binding protein 2

Pescadillo homolog

60S ribosomal protein L43-A

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Ribosome biogenesis protein RLP24

Ribosome biogenesis protein RPF2

Regulator of ribosome biosynthesis

Ribosome assembly protein 4

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

Probable metalloprotease ARX1

rRNA-processing protein CGR1

Exosome complex exonuclease RRP6

Exosome complex protein LRP1

ATP-dependent RNA helicase DOB1

MPP6

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