SMTL ID : 3jct.1

Cryo-em structure of eukaryotic pre-60S ribosomal subunits

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain I: C.51, C.54, H.67, H.73 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.51, I:C.54, I: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: 6 residues within 4Å: Chain f: C.39, F.41, C.42, C.57, C.59, C.60 2 PLIP interactions: 2 interactions with chain f Metal complexes: f:C.39, f:C.42 ZN.8: 6 residues within 4Å: Chain k: C.9, C.32, R.33, K.35, C.36, W.51 1 PLIP interactions: 1 interactions with chain k Metal complexes: k:C.36

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

GTP.2: 23 residues within 4Å: Chain 1: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, D.193, V.194, P.196, A.198, T.200, T.201, D.220, P.222, N.288, K.289, D.291, S.321, C.322, Q.323 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain 1 Hydrogen bonds: 1:Y.175, 1:N.177, 1:V.178, 1:G.179, 1:G.179, 1:K.180, 1:S.181, 1:S.181, 1:S.182, 1:T.201, 1:T.201, 1:T.201, 1:K.289, 1:C.322, 1:Q.323, 1:Q.323, 1:Q.323, 1:Q.323 Salt bridges: 1:D.291 GTP.5: 22 residues within 4Å: Ligands: MG.6 Chain c: N.260, K.261, D.263, L.264, H.287, A.288, P.324, N.325, T.326, G.327, K.328, S.329, S.330, Q.342, V.343, A.344, P.345, P.347, E.349, T.350 Chain q: U.2318 19 PLIP interactions: 18 interactions with chain c, 1 interactions with chain l Hydrogen bonds: c:N.260, c:K.261, c:K.261, c:H.287, c:A.288, c:N.325, c:T.326, c:G.327, c:K.328, c:S.329, c:S.329, c:S.330, c:S.330, c:A.344, c:A.344, c:E.349, c:T.350, l:R.288 Salt bridges: c:D.263

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain 1: Q.195, Y.197, T.200 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain 1 Metal complexes: 1:Q.195, 1:T.200 MG.6: 4 residues within 4Å: Ligands: GTP.5 Chain c: A.344, I.346, P.347 1 PLIP interactions: 1 interactions with chain c Metal complexes: c:I.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, S. et al., Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Nature (2016)

Release Date

2016-06-01

Peptides

60S ribosomal protein L2-A: A
60S ribosomal protein L3: B
60S ribosomal protein L4-A: C
60S ribosomal protein L5: D
60S ribosomal protein L6-A: E
60S ribosomal protein L7-A: F
60S ribosomal protein L8-A: G
60S ribosomal protein L9-A: H
Bud site selection protein 20: I
60S ribosomal protein L11-A: J
Proteasome-interacting protein CIC1: 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
Ribosome biogenesis protein 15: e
60S ribosomal protein L43-A: f
Ribosome biogenesis protein NOP53: g
Ribosome biogenesis protein NSA2: h
Nuclear GTP-binding protein NUG1: i
Ribosome biogenesis protein RLP7: j
Ribosome biogenesis protein RLP24: k
Ribosome biogenesis protein RPF2: l
Regulator of ribosome biosynthesis: m
Ribosome assembly protein 4: n
Eukaryotic translation initiation factor 6: o
UPF0642 protein YBL028C: p
Probable metalloprotease ARX1: t
rRNA-processing protein CGR1: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

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
o

f
p

g
q

h
r

i
s

j
t

k
u

l
v

m
w

n
x

o
y

p
z

t
4

u
5

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

Proteasome-interacting protein CIC1

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

Ribosome biogenesis protein 15

60S ribosomal protein L43-A

Ribosome biogenesis protein NOP53

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Ribosome biogenesis protein RLP7

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

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