SMTL ID : 8v83.1

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)

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

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 6 residues within 4Å: Chain h: C.6, C.9, S.11, C.32, R.33, C.36 3 PLIP interactions: 3 interactions with chain h Metal complexes: h:C.6, h:C.32, h:C.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cruz, V.E. et al., The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis. Nat Commun (2024)

Release Date

2024-05-01

Peptides

60S ribosomal subunit assembly/export protein LOC1: D
Ribosomal RNA-processing protein 14: E
Ribosome biogenesis protein BRX1: F
60S ribosomal protein L3: G
60S ribosomal protein L4-A: H
ATP-dependent RNA helicase HAS1: I
60S ribosomal protein L6-A: J
60S ribosomal protein L7-A: K
Large ribosomal subunit protein eL8A: L
Large ribosomal subunit protein uL6A: M
Ribosome biogenesis protein NSA1: N
rRNA-processing protein EBP2: O
Proteasome-interacting protein CIC1: P
60S ribosomal protein L13-A: Q
60S ribosomal protein L14-A: R
Large ribosomal subunit protein eL15A: S
Large ribosomal subunit protein uL13A: T
60S ribosomal protein L17-A: U
60S ribosomal protein L18-A: V
Protein MAK16: W
Large ribosomal subunit protein eL20A: X
Ribosomal RNA-processing protein 15: Y
60S ribosomal protein L23-A: Z
Ribosome assembly factor MRT4: 0
60S ribosomal protein L26-A: 1
Ribosome biogenesis protein SSF1: 2
Large ribosomal subunit protein uL1A: 3
Nucleolar GTP-binding protein 1: 4
60S ribosomal protein L32: 5
60S ribosomal protein L33-A: 6
60S ribosomal protein L35-A: 7
60S ribosomal protein L36-A: 8
60S ribosomal protein L37-A: 9
60S ribosome subunit biogenesis protein NIP7: a
Ribosome biogenesis protein ERB1: b
Pescadillo homolog: c
Ribosome biogenesis protein 15: d
25S rRNA (cytosine(2870)-C(5))-methyltransferase: e
Ribosome biogenesis protein NSA2: f
Ribosome biogenesis protein RLP7: g
Ribosome biogenesis protein RLP24: h
Nucleolar protein 16: i
Ribosomal RNA-processing protein 1: j
Ribosome production factor 1: k
Eukaryotic translation initiation factor 6: l

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
T

Z
V

0
W

1
Y

2
Z

3
a

4
b

5
e

6
f

7
h

8
i

9
j

a
l

b
m

c
n

d
o

e
q

f
r

g
t

h
u

i
v

j
w

k
x

l
y

60S ribosomal subunit assembly/export protein LOC1

Ribosomal RNA-processing protein 14

Ribosome biogenesis protein BRX1

60S ribosomal protein L3

60S ribosomal protein L4-A

ATP-dependent RNA helicase HAS1

60S ribosomal protein L6-A

60S ribosomal protein L7-A

Large ribosomal subunit protein eL8A

Large ribosomal subunit protein uL6A

Ribosome biogenesis protein NSA1

rRNA-processing protein EBP2

Proteasome-interacting protein CIC1

60S ribosomal protein L13-A

60S ribosomal protein L14-A

Large ribosomal subunit protein eL15A

Large ribosomal subunit protein uL13A

60S ribosomal protein L17-A

60S ribosomal protein L18-A

Protein MAK16

Large ribosomal subunit protein eL20A

Ribosomal RNA-processing protein 15

60S ribosomal protein L23-A

Ribosome assembly factor MRT4

60S ribosomal protein L26-A

Ribosome biogenesis protein SSF1

Large ribosomal subunit protein uL1A

Nucleolar GTP-binding protein 1

60S ribosomal protein L32

60S ribosomal protein L33-A

60S ribosomal protein L35-A

60S ribosomal protein L36-A

60S ribosomal protein L37-A

60S ribosome subunit biogenesis protein NIP7

Ribosome biogenesis protein ERB1

Pescadillo homolog

Ribosome biogenesis protein 15

25S rRNA (cytosine(2870)-C(5))-methyltransferase

Ribosome biogenesis protein NSA2

Ribosome biogenesis protein RLP7

Ribosome biogenesis protein RLP24

Nucleolar protein 16

Ribosomal RNA-processing protein 1

Ribosome production factor 1

Eukaryotic translation initiation factor 6

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