SMTL ID : 8v84.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GDP.1: 16 residues within 4Å: Chain 5: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, V.194, Q.195, P.196, T.200, Q.259, N.288, C.322, Q.323 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain 5 Hydrogen bonds: 5:N.177, 5:V.178, 5:G.179, 5:S.181, 5:V.194, 5:T.200, 5:T.200, 5:Q.259, 5:C.322, 5:Q.323 Salt bridges: 5:K.180

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain 5: S.181, T.200, T.201 Ligands: GDP.1 2 PLIP interactions: 2 interactions with chain 5 Metal complexes: 5:S.181, 5:T.200

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain a: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.19, a:C.22, a:C.34, a:C.37 ZN.4: 6 residues within 4Å: Chain i: C.6, C.9, S.11, C.32, R.33, C.36 3 PLIP interactions: 3 interactions with chain i Metal complexes: i:C.6, i:C.32, i: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

ATP-dependent RNA helicase DBP10: C
60S ribosomal subunit assembly/export protein LOC1: E
Ribosomal RNA-processing protein 14: F
Ribosome biogenesis protein BRX1: G
Large ribosomal subunit protein uL3: H
60S ribosomal protein L4-A: I
ATP-dependent RNA helicase HAS1: J
60S ribosomal protein L6-A: K
60S ribosomal protein L7-A: L
Large ribosomal subunit protein eL8A: M
Large ribosomal subunit protein uL6A: N
Ribosome biogenesis protein NSA1: O
rRNA-processing protein EBP2: P
Proteasome-interacting protein CIC1: Q
60S ribosomal protein L13-A: R
60S ribosomal protein L14-A: S
Large ribosomal subunit protein eL15A: T
Large ribosomal subunit protein uL13A: U
60S ribosomal protein L17-A: V
60S ribosomal protein L18-A: W
Protein MAK16: X
Large ribosomal subunit protein eL20A: Y
Ribosomal RNA-processing protein 15: Z
60S ribosomal protein L23-A: 0
Ribosome assembly factor MRT4: 1
60S ribosomal protein L26-A: 2
Ribosome biogenesis protein SSF1: 3
Large ribosomal subunit protein uL1A: 4
Nucleolar GTP-binding protein 1: 5
60S ribosomal protein L32: 6
60S ribosomal protein L33-A: 7
60S ribosomal protein L35-A: 8
60S ribosomal protein L36-A: 9
60S ribosomal protein L37-A: a
60S ribosome subunit biogenesis protein NIP7: b
Ribosome biogenesis protein ERB1: c
Pescadillo homolog: d
Ribosome biogenesis protein 15: e
25S rRNA (cytosine(2870)-C(5))-methyltransferase: f
Ribosome biogenesis protein NSA2: g
Ribosome biogenesis protein RLP7: h
Ribosome biogenesis protein RLP24: i
Nucleolar protein 16: j
Ribosomal RNA-processing protein 1: k
Ribosome production factor 1: l
Eukaryotic translation initiation factor 6: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
3

E
7

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
T

0
V

1
W

2
Y

3
Z

4
a

5
b

6
e

7
f

8
h

9
i

a
j

b
l

c
m

d
n

e
o

f
q

g
r

h
t

i
u

j
v

k
w

l
x

m
y

ATP-dependent RNA helicase DBP10

60S ribosomal subunit assembly/export protein LOC1

Ribosomal RNA-processing protein 14

Ribosome biogenesis protein BRX1

Large ribosomal subunit protein uL3

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

Related Entries With Identical Sequence