SMTL ID : 8esr.1

Ytm1 associated nascent 60S ribosome (-fkbp39) State 2

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-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain d: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.19, d:C.22, d:C.34, d:C.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ugolini, I. et al., Chromatin localization of nucleophosmin organizes ribosome biogenesis. Mol.Cell (2022)

Release Date

2022-11-30

Peptides

Noc2: D
60S ribosomal protein L39: E
Ribosome biogenesis protein brx1: F
60S ribosomal protein L3-A: G
60S ribosomal protein L4-B: H
ATP-dependent RNA helicase has1: I
60S ribosomal protein L6: J
60S ribosomal protein L7-B: K
60S ribosomal protein L8: L
60S ribosomal protein L9-A: M
Nucleolar complex-associated protein 3: N
Probable rRNA-processing protein ebp2: O
Putative ribosome biogenesis protein C8F11.04: P
60S ribosomal protein L13: Q
60S ribosomal protein L14: R
60S ribosomal protein L15-A: S
60S ribosomal protein L16-B: T
60S ribosomal protein L17-A: U
60S ribosomal protein L18-A: V
60S ribosomal protein L19-A: W
60S ribosomal protein L20-A: X
60S ribosomal protein L22: Y
60S ribosomal protein L23-A: Z
Ribosome assembly factor mrt4: 0
60S ribosomal protein L25-A: 1
60S ribosomal protein L26: 2
60S ribosomal protein L27-A: 3
60S ribosomal protein L28-A: 4
Probable nucleolar GTP-binding protein 1: 5
60S ribosomal protein L30-2: 6
60S ribosomal protein L31: 7
60S ribosomal protein L32-A: 8
60S ribosomal protein L33-B: 9
60S ribosomal protein L34-A: a
60S ribosomal protein L35: b
60S ribosomal protein L36-B: c
60S ribosomal protein L37-B: d
60S ribosomal protein L38-1: e
60S ribosome subunit biogenesis protein nip7: f
Ribosome biogenesis protein erb1: g
Pescadillo homolog: h
Uncharacterized RNA-binding protein C1827.05c: i
Ribosome biogenesis protein ytm1: j
25S rRNA (cytosine-C(5))-methyltransferase nop2: k
Ribosome biogenesis protein nsa2: l
GTPase grn1: m
60S ribosomal protein L7-A: n
Ribosome biogenesis protein rlp24: o
Nucleolar protein 16: p
AdoMet-dependent rRNA methyltransferase spb1: q
Eukaryotic translation initiation factor 6: r
UPF0642 protein C32H8.05: s
60S ribosomal protein L21-A: t

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
7

E
8

F
A

G
B

H
C

I
D

J
E

K
F

L
G

M
H

N
I

O
J

P
K

Q
L

R
M

S
N

T
O

U
P

V
Q

W
R

X
S

Y
U

Z
V

0
W

1
X

2
Y

3
Z

4
a

5
b

6
c

7
d

8
e

9
f

a
g

b
h

c
i

d
j

e
k

f
l

g
m

h
n

i
o

j
p

k
q

l
r

m
s

n
t

o
u

p
v

q
w

r
y

s
z

t
T

Noc2

60S ribosomal protein L39

Ribosome biogenesis protein brx1

60S ribosomal protein L3-A

60S ribosomal protein L4-B

ATP-dependent RNA helicase has1

60S ribosomal protein L6

60S ribosomal protein L7-B

60S ribosomal protein L8

60S ribosomal protein L9-A

Nucleolar complex-associated protein 3

Probable rRNA-processing protein ebp2

Putative ribosome biogenesis protein C8F11.04

60S ribosomal protein L13

60S ribosomal protein L14

60S ribosomal protein L15-A

60S ribosomal protein L16-B

60S ribosomal protein L17-A

60S ribosomal protein L18-A

60S ribosomal protein L19-A

60S ribosomal protein L20-A

60S ribosomal protein L22

60S ribosomal protein L23-A

Ribosome assembly factor mrt4

60S ribosomal protein L25-A

60S ribosomal protein L26

60S ribosomal protein L27-A

60S ribosomal protein L28-A

Probable nucleolar GTP-binding protein 1

60S ribosomal protein L30-2

60S ribosomal protein L31

60S ribosomal protein L32-A

60S ribosomal protein L33-B

60S ribosomal protein L34-A

60S ribosomal protein L35

60S ribosomal protein L36-B

60S ribosomal protein L37-B

60S ribosomal protein L38-1

60S ribosome subunit biogenesis protein nip7

Ribosome biogenesis protein erb1

Pescadillo homolog

Uncharacterized RNA-binding protein C1827.05c

Ribosome biogenesis protein ytm1

25S rRNA (cytosine-C(5))-methyltransferase nop2

Ribosome biogenesis protein nsa2

GTPase grn1

60S ribosomal protein L7-A

Ribosome biogenesis protein rlp24

Nucleolar protein 16

AdoMet-dependent rRNA methyltransferase spb1

Eukaryotic translation initiation factor 6

UPF0642 protein C32H8.05

60S ribosomal protein L21-A

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