7uoo.1 | SWISS-MODEL Template Library

SMTL ID : 7uoo.1

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

81 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

3 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)(Non-covalent)

5 x ZN: ZINC ION(Non-covalent)

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

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

GTP.88:

25 residues within 4Å:

25 PLIP interactions:

1 x K: POTASSIUM ION(Non-covalent)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sekulski, K. et al., rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly. Nat Commun (2023)

Release Date

2023-03-15

Peptides

60S ribosomal protein L2-A: A
rRNA-processing protein: E
60S ribosomal protein L12-A: G
Ribosome biogenesis protein ALB1: H
60S ribosomal protein L3: I
60S ribosomal protein L4-A: J
60S ribosomal protein L5: K
60S ribosomal protein L6-A: L
60S ribosomal protein L7-A: M
60S ribosomal protein L8-A: N
60S ribosomal protein L9-A: O
Bud site selection protein 20: P
60S ribosomal protein L11-A: Q
Proteasome-interacting protein CIC1: R
60S ribosomal protein L13-A: S
60S ribosomal protein L14-A: T
60S ribosomal protein L15-A: U
60S ribosomal protein L16-A: V
60S ribosomal protein L17-A: W
60S ribosomal protein L18-A: X
60S ribosomal protein L19-A: Y
60S ribosomal protein L20-A: Z
60S ribosomal protein L21-A: 0
60S ribosomal protein L22-A: 1
60S ribosomal protein L23-A: 2
Ribosome assembly factor MRT4: 3
60S ribosomal protein L25: 4
60S ribosomal protein L26-A: 5
60S ribosomal protein L27-A: 6
60S ribosomal protein L28: 7
Nucleolar GTP-binding protein 1: 8
60S ribosomal protein L30: 9
60S ribosomal protein L31-A: a
60S ribosomal protein L32: b
60S ribosomal protein L33-A: c
60S ribosomal protein L34-A: d
60S ribosomal protein L35-A: e
60S ribosomal protein L36-A: f
60S ribosomal protein L37-A: g
60S ribosomal protein L38: h
60S ribosomal protein L39: i
Nucleolar GTP-binding protein 2: j
Pescadillo homolog: k
Ribosome biogenesis protein 15: l
60S ribosomal protein L43-A: m
Ribosome biogenesis protein NOP53: n
Ribosome biogenesis protein NSA2: o
Nuclear GTP-binding protein NUG1: p
Ribosome biogenesis protein RLP7: q
Ribosome biogenesis protein RLP24: r
Ribosome production factor 2 homolog: s
Ribosome biogenesis regulatory protein: t
RSA4 isoform 1: u
Eukaryotic translation initiation factor 6: v
UPF0642 protein YBL028C: w
Probable metalloprotease ARX1: x

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
5

G
8

H
9

I
B

J
C

K
D

L
E

M
F

N
G

O
H

P
I

Q
J

R
K

S
L

T
M

U
N

V
O

W
P

X
Q

Y
R

Z
S

0
T

1
U

2
V

3
W

4
X

5
Y

6
Z

7
a

8
b

9
c

a
d

b
e

c
f

d
g

e
h

f
i

g
j

h
k

i
l

j
m

k
n

l
o

m
p

n
q

o
r

p
s

q
t

r
u

s
v

t
w

u
x

v
y

w
z

x
4

60S ribosomal protein L2-A

rRNA-processing protein

60S ribosomal protein L12-A

Ribosome biogenesis protein ALB1

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 production factor 2 homolog

Ribosome biogenesis regulatory protein

RSA4 isoform 1

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

Probable metalloprotease ARX1

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