SMTL ID : 8idt.1

human nuclear pre-60S ribosomal particle - State G

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-mer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 17 residues within 4Å: Ligands: MG.2, K.3 Chain d: N.255, K.256, D.258, L.259, H.282, A.283, N.320, V.321, G.322, K.323, S.324, S.325, V.338, A.339, P.340 16 PLIP interactions: 16 interactions with chain d Hydrogen bonds: d:N.255, d:K.256, d:K.256, d:A.283, d:N.320, d:V.321, d:G.322, d:K.323, d:S.324, d:S.324, d:S.325, d:S.325, d:A.339, d:P.340 Salt bridges: d:D.258, d:K.323

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Ligands: GDP.1 Chain d: S.324, T.345 2 PLIP interactions: 2 interactions with chain d Metal complexes: d:S.324, d:T.345 MG.5: 5 residues within 4Å: Ligands: GTP.4 Chain j: N.178, Q.196, Y.198, T.201 1 PLIP interactions: 1 interactions with chain j Metal complexes: j:Q.196

1 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Ligands: GDP.1 Chain d: N.320, A.339, I.341 2 PLIP interactions: 2 interactions with chain d Metal complexes: d:A.339, d:I.341

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.4: 21 residues within 4Å: Ligands: MG.5 Chain j: P.177, N.178, V.179, G.180, K.181, S.182, S.183, V.193, D.194, V.195, Q.196, P.197, T.201, T.202, D.221, N.289, K.290, S.321, T.322, L.323 16 PLIP interactions: 16 interactions with chain j Hydrogen bonds: j:N.178, j:V.179, j:G.180, j:G.180, j:K.181, j:S.182, j:S.183, j:Q.196, j:T.202, j:N.289, j:T.322, j:T.322, j:L.323 Salt bridges: j:K.181, j:K.181, j:D.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles. Cell Res. (2023)

Release Date

2023-08-09

Peptides

Eukaryotic translation initiation factor 6: B
Probable ribosome biogenesis protein RLP24: C
Zinc finger protein 593: E
60S ribosomal protein L3: F
60S ribosomal protein L29: G
60S ribosomal protein L4: H
60S ribosomal protein L30: I
60S ribosomal protein L34: J
60S ribosomal protein L7a: K
60S ribosomal protein L35: L
60S ribosomal protein L9: M
60S ribosomal protein L36: N
60S ribosomal protein L27a: O
60S ribosomal protein L37: P
60S ribosomal protein L11: Q
60S ribosomal protein L38: R
60S ribosomal protein L39: S
60S ribosomal protein L13: T
60S ribosomal protein L14: U
60S ribosomal protein L15: V
60S ribosomal protein L13a: W
60S ribosomal protein L36a: X
60S ribosomal protein L37a: Y
60S ribosomal protein L18: Z
60S ribosomal protein L19: 0
60S ribosomal protein L18a: 1
60S ribosomal protein L21: 2
60S ribosomal protein L23: 3
60S ribosomal protein L23a: 4
60S ribosomal protein L26: 5
60S ribosomal protein L27: 6
60S ribosomal protein L28: 7
60S ribosomal protein L8: 8
60S ribosomal protein L35a: 9
60S ribosomal protein L6: a
60S ribosomal protein L7: b
60S ribosomal protein L5: c
G Protein Nucleolar 2: d
Translation machinery-associated protein 16: e
mRNA turnover protein 4 homolog: f
Leydig cell tumor 10 kDa protein homolog: g
60S ribosomal protein L12: i
GTP-binding protein 4: j
60S ribosomal protein L22: k
60S ribosomal protein L31: l
60S ribosomal protein L32: m
60S ribosomal protein L17: n
Protein LLP homolog: o

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
6

C
7

E
9

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
K

O
L

P
M

Q
N

R
O

S
P

T
Q

U
S

V
U

W
V

X
W

Y
X

Z
Z

0
a

1
b

2
c

3
e

4
g

5
h

6
i

7
l

8
m

9
n

a
o

b
p

c
r

d
A

e
R

f
J

g
T

i
y

j
4

k
d

l
j

m
k

n
Y

o
z

Eukaryotic translation initiation factor 6

Probable ribosome biogenesis protein RLP24

Zinc finger protein 593

60S ribosomal protein L3

60S ribosomal protein L29

60S ribosomal protein L4

60S ribosomal protein L30

60S ribosomal protein L34

60S ribosomal protein L7a

60S ribosomal protein L35

60S ribosomal protein L9

60S ribosomal protein L36

60S ribosomal protein L27a

60S ribosomal protein L37

60S ribosomal protein L11

60S ribosomal protein L38

60S ribosomal protein L39

60S ribosomal protein L13

60S ribosomal protein L14

60S ribosomal protein L15

60S ribosomal protein L13a

60S ribosomal protein L36a

60S ribosomal protein L37a

60S ribosomal protein L18

60S ribosomal protein L19

60S ribosomal protein L18a

60S ribosomal protein L21

60S ribosomal protein L23

60S ribosomal protein L23a

60S ribosomal protein L26

60S ribosomal protein L27

60S ribosomal protein L28

60S ribosomal protein L8

60S ribosomal protein L35a

60S ribosomal protein L6

60S ribosomal protein L7

60S ribosomal protein L5

G Protein Nucleolar 2

Translation machinery-associated protein 16

mRNA turnover protein 4 homolog

Leydig cell tumor 10 kDa protein homolog

60S ribosomal protein L12

GTP-binding protein 4

60S ribosomal protein L22

60S ribosomal protein L31

60S ribosomal protein L32

60S ribosomal protein L17

Protein LLP homolog

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