SMTL ID : 8esq.1

Ytm1 associated nascent 60S ribosome State 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain e: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain e Metal complexes: e:C.19, e:C.22, e:C.34, e: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: A
Protein mak16: D
60S ribosomal protein L39: F
Ribosome biogenesis protein brx1: G
60S ribosomal protein L3-A: H
60S ribosomal protein L4-B: I
ATP-dependent RNA helicase has1: J
60S ribosomal protein L6: K
60S ribosomal protein L7-B: L
60S ribosomal protein L8: M
60S ribosomal protein L9-A: N
Nucleolar complex-associated protein 3: O
Probable rRNA-processing protein ebp2: P
Putative ribosome biogenesis protein C8F11.04: Q
60S ribosomal protein L13: R
60S ribosomal protein L14: S
60S ribosomal protein L15-A: T
60S ribosomal protein L16-B: U
60S ribosomal protein L17-A: V
60S ribosomal protein L18-A: W
60S ribosomal protein L19-A: X
60S ribosomal protein L20-A: Y
60S ribosomal protein L22: Z
60S ribosomal protein L23-A: 0
Ribosome assembly factor mrt4: 1
60S ribosomal protein L25-A: 2
60S ribosomal protein L26: 3
60S ribosomal protein L27-A: 4
60S ribosomal protein L28-A: 5
Probable nucleolar GTP-binding protein 1: 6
60S ribosomal protein L30-2: 7
60S ribosomal protein L31: 8
60S ribosomal protein L32-A: 9
60S ribosomal protein L33-B: a
60S ribosomal protein L34-A: b
60S ribosomal protein L35: c
60S ribosomal protein L36-B: d
60S ribosomal protein L37-B: e
60S ribosomal protein L38-1: f
60S ribosome subunit biogenesis protein nip7: g
Ribosome biogenesis protein erb1: h
Pescadillo homolog: i
Uncharacterized RNA-binding protein C1827.05c: j
Ribosome biogenesis protein ytm1: k
25S rRNA (cytosine-C(5))-methyltransferase nop2: l
Ribosome biogenesis protein nsa2: m
GTPase grn1: n
60S ribosomal protein L7-A: o
Ribosome biogenesis protein rlp24: p
Nucleolar protein 16: q
AdoMet-dependent rRNA methyltransferase spb1: r
Brix domain-containing protein C4F8.04: s
Eukaryotic translation initiation factor 6: t
UPF0642 protein C32H8.05: u
60S ribosomal protein L21-A: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
7

D
3

F
8

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

O
I

P
J

Q
K

R
L

S
M

T
N

U
O

V
P

W
Q

X
R

Y
S

Z
U

0
V

1
W

2
X

3
Y

4
Z

5
a

6
b

7
c

8
d

9
e

a
f

b
g

c
h

d
i

e
j

f
k

g
l

h
m

i
n

j
o

k
p

l
q

m
r

n
s

o
t

p
u

q
v

r
w

s
x

t
y

u
z

v
T

Noc2

Protein mak16

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

Brix domain-containing protein C4F8.04

Eukaryotic translation initiation factor 6

UPF0642 protein C32H8.05

60S ribosomal protein L21-A

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