SMTL ID : 6n8j.1

Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit

Coordinates

PDB Format

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-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain F: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, V.194, P.196, Y.197, A.198, T.200, T.201, D.220, P.222, N.288, K.289, D.291, I.292, S.321, C.322 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:N.177, F:N.177, F:V.178, F:G.179, F:K.180, F:S.181, F:S.182, F:T.201, F:T.201, F:T.201, F:N.288, F:K.289, F:C.322 Salt bridges: F:K.180, F:K.180, F:D.291 GTP.3: 17 residues within 4Å: Chain V: K.261, H.287, A.288, N.325, G.327, K.328, S.329, S.330, Q.342, V.343, A.344, P.345, P.347, E.349, T.350, C.367 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain V Hydrogen bonds: V:K.261, V:A.288, V:N.325, V:G.327, V:K.328, V:S.329, V:S.329, V:A.344, V:A.344, V:E.349, V:T.350, V:C.367 Salt bridges: V:K.328, V:K.328 pi-Cation interactions: V:K.261

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain F: N.177, Q.195, Y.197 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:Q.195 MG.4: 3 residues within 4Å: Chain V: N.325, A.344 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Nat Commun (2019)

Release Date

2019-03-13

Peptides

60S ribosomal protein L5: A
60S ribosomal protein L11-A: B
60S ribosomal protein L2-A: C
60S ribosomal protein L28: D
60S ribosomal protein L3: E
Nucleolar GTP-binding protein 1: F
60S ribosomal protein L4-A: G
60S ribosomal protein L30: H
60S ribosomal protein L31-A: I
60S ribosomal protein L6-A: J
60S ribosomal protein L32: K
60S ribosomal protein L7-A: L
60S ribosomal protein L33-A: M
60S ribosomal protein L8-A: N
60S ribosomal protein L34-A: O
Bud site selection protein 20: P
60S ribosomal protein L9-A: Q
60S ribosomal protein L35-A: R
60S ribosomal protein L36-A: S
60S ribosomal protein L37-A: T
60S ribosomal protein L38: U
Nucleolar GTP-binding protein 2: V
60S ribosomal protein L13-A: W
60S ribosomal protein L39: X
60S ribosomal protein L14-A: Y
60S ribosomal protein L43-A: Z
60S ribosomal protein L15-A: 0
Ribosome biogenesis protein RLP24: 1
60S ribosomal protein L16-A: 2
60S ribosomal protein L17-A: 3
60S ribosomal protein L18-A: 4
60S ribosomal protein L19-A: 5
Ribosome biogenesis protein NSA2: 6
60S ribosomal protein L20-A: 7
60S ribosomal protein L21-A: 8
60S ribosomal protein L22-A: 9
60S ribosomal protein L23-A: a
Ribosome assembly factor MRT4: b
60S ribosomal protein L25: c
60S ribosomal protein L26-A: d
Eukaryotic translation initiation factor 6: e
60S ribosomal protein L27-A: f
UPF0642 protein YBL028C: g
60S ribosomal protein L12: h
60S ribosomal protein L42-A: i
60S ribosomal protein L29: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
J

C
A

D
a

E
B

F
b

G
C

H
c

I
d

J
E

K
e

L
F

M
f

N
G

O
g

P
I

Q
H

R
h

S
i

T
j

U
k

V
m

W
L

X
l

Y
M

Z
p

0
N

1
u

2
O

3
P

4
Q

5
R

6
r

7
S

8
T

9
U

a
V

b
W

c
X

d
Y

e
y

f
Z

g
z

h
K

i
q

j
o

60S ribosomal protein L5

60S ribosomal protein L11-A

60S ribosomal protein L2-A

60S ribosomal protein L28

60S ribosomal protein L3

Nucleolar GTP-binding protein 1

60S ribosomal protein L4-A

60S ribosomal protein L30

60S ribosomal protein L31-A

60S ribosomal protein L6-A

60S ribosomal protein L32

60S ribosomal protein L7-A

60S ribosomal protein L33-A

60S ribosomal protein L8-A

60S ribosomal protein L34-A

Bud site selection protein 20

60S ribosomal protein L9-A

60S ribosomal protein L35-A

60S ribosomal protein L36-A

60S ribosomal protein L37-A

60S ribosomal protein L38

Nucleolar GTP-binding protein 2

60S ribosomal protein L13-A

60S ribosomal protein L39

60S ribosomal protein L14-A

60S ribosomal protein L43-A

60S ribosomal protein L15-A

Ribosome biogenesis protein RLP24

60S ribosomal protein L16-A

60S ribosomal protein L17-A

60S ribosomal protein L18-A

60S ribosomal protein L19-A

Ribosome biogenesis protein NSA2

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

Eukaryotic translation initiation factor 6

60S ribosomal protein L27-A

UPF0642 protein YBL028C

60S ribosomal protein L12

60S ribosomal protein L42-A

60S ribosomal protein L29

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