SMTL ID : 8euy.1

Ytm1 associated nascent 60S ribosome (-fkbp39) State 1A

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-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

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

Protein mak16: C
Ribosomal RNA-processing protein 1 homolog: D
Ribosome biogenesis protein nsa1: E
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
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 L20-A: W
60S ribosomal protein L23-A: X
60S ribosomal protein L26: Y
Probable nucleolar GTP-binding protein 1: Z
60S ribosomal protein L32-A: 0
60S ribosomal protein L33-B: 1
60S ribosomal protein L35: 2
60S ribosomal protein L36-B: 3
60S ribosomal protein L37-B: 4
Ribosome biogenesis protein erb1: 5
Uncharacterized RNA-binding protein C1827.05c: 6
Ribosome biogenesis protein nsa2: 7
60S ribosomal protein L7-A: 8
Ribosome biogenesis protein rlp24: 9
Nucleolar protein 16: a
Brix domain-containing protein C4F8.04: b
Eukaryotic translation initiation factor 6: c
60S ribosomal protein L21-A: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
3

D
4

E
5

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

O
J

P
K

Q
L

R
M

S
N

T
O

U
P

V
Q

W
S

X
V

Y
Y

Z
b

0
e

1
f

2
h

3
i

4
j

5
m

6
o

7
r

8
t

9
u

a
v

b
x

c
y

d
T

Protein mak16

Ribosomal RNA-processing protein 1 homolog

Ribosome biogenesis protein nsa1

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

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 L20-A

60S ribosomal protein L23-A

60S ribosomal protein L26

Probable nucleolar GTP-binding protein 1

60S ribosomal protein L32-A

60S ribosomal protein L33-B

60S ribosomal protein L35

60S ribosomal protein L36-B

60S ribosomal protein L37-B

Ribosome biogenesis protein erb1

Uncharacterized RNA-binding protein C1827.05c

Ribosome biogenesis protein nsa2

60S ribosomal protein L7-A

Ribosome biogenesis protein rlp24

Nucleolar protein 16

Brix domain-containing protein C4F8.04

Eukaryotic translation initiation factor 6

60S ribosomal protein L21-A

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