SMTL ID : 7u0h.1

State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model

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-mer

Ligands

1 x ASN- LEU- GLU- ASP- LEU- VAL- LYS- ALA- THR: Nucleolar GTP-binding protein 2(Non-covalent)

ASN-LEU-GLU-ASP-LEU-VAL-LYS-ALA-THR.1: 5 residues within 4Å: Chain 1: A.244, H.245, S.273, P.276, L.277 3 PLIP interactions: 3 interactions with chain 1 Hydrophobic interactions: 1:A.244, 1:L.277, 1:L.277

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain 1: P.176, N.177, Q.195, Y.197, T.200 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:Y.197

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain 6: C.44, C.47, C.81, C.84 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.44, 6:C.47, 6:C.81, 6:C.84 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.5: 5 residues within 4Å: Chain d: C.39, C.42, C.57, C.59, C.60 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.39, d:C.42, d:C.57, d:C.60 ZN.6: 4 residues within 4Å: Chain i: R.33, K.35, C.36, W.51 1 PLIP interactions: 1 interactions with chain i Metal complexes: i:C.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cruz, V.E. et al., Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-12-14

Peptides

60S ribosomal protein L2-A: D
60S ribosomal protein L3: E
60S ribosomal protein L4-A: F
60S ribosomal protein L6-A: G
60S ribosomal protein L7-A: H
60S ribosomal protein L8-A: I
60S ribosomal protein L9-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
Pescadillo homolog: b
Ribosome biogenesis protein 15: c
60S ribosomal protein L43-A: d
Ribosome biogenesis protein NOP53: e
Ribosome biogenesis protein NSA2: f
Nuclear GTP-binding protein NUG1: g
Ribosome biogenesis protein RLP7: h
Ribosome biogenesis protein RLP24: i
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase: j
Eukaryotic translation initiation factor 6: k
UPF0642 protein YBL028C: l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
E

H
F

I
G

J
H

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
n

c
o

d
p

e
q

f
r

g
s

h
t

i
u

j
w

k
y

l
z

60S ribosomal protein L2-A

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L6-A

60S ribosomal protein L7-A

60S ribosomal protein L8-A

60S ribosomal protein L9-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

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

27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

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