SMTL ID : 8v87.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 11 residues within 4Å: Chain C: F.157, Q.159, T.161, R.182, T.183, G.184, S.185, G.186, K.187, T.188 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.164, C:R.182, C:G.184, C:S.185, C:G.186, C:K.187, C:T.188 Salt bridges: C:K.187 pi-Stacking: C:F.157

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: T.188, E.289 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain 6: S.181, T.201 Ligands: GDP.3 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:T.201

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

GDP.3: 18 residues within 4Å: Chain 6: Y.175, N.177, V.178, G.179, K.180, S.181, S.182, V.194, Q.195, P.196, Q.259, N.288, K.289, D.291, S.321, C.322 Ligands: K.4, MG.5 13 PLIP interactions: 13 interactions with chain 6 Hydrogen bonds: 6:N.177, 6:V.178, 6:G.179, 6:K.180, 6:S.181, 6:S.182, 6:Q.195, 6:Q.259, 6:N.288, 6:K.289, 6:C.322 Salt bridges: 6:K.180, 6:D.291

1 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain 6: Q.195, Y.197, A.198, T.200 Ligands: GDP.3 2 PLIP interactions: 2 interactions with chain 6 Metal complexes: 6:Y.197, 6:T.200

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain b: D.46, C.47, C.84 1 PLIP interactions: 1 interactions with chain b Metal complexes: b:C.84 ZN.7: 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

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
Nucleolar complex protein 2: F
Ribosome biogenesis protein BRX1: G
60S ribosomal protein L3: 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
Nucleolar complex-associated protein 3: 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
60S ribosomal protein L19-A: X
Large ribosomal subunit protein eL20A: Y
60S ribosomal protein L22-A: Z
60S ribosomal protein L23-A: 0
Ribosome assembly factor MRT4: 1
60S ribosomal protein L25: 2
60S ribosomal protein L26-A: 3
60S ribosomal protein L27-A: 4
Large ribosomal subunit protein uL1A: 5
Nucleolar GTP-binding protein 1: 6
60S ribosomal protein L30: 7
60S ribosomal protein L31-A: 8
60S ribosomal protein L32: 9
60S ribosomal protein L33-A: a
60S ribosomal protein L34-A: b
60S ribosomal protein L35-A: c
60S ribosomal protein L36-A: d
60S ribosomal protein L37-A: e
60S ribosomal protein L38: f
60S ribosome subunit biogenesis protein NIP7: g
Ribosome biogenesis protein ERB1: h
Pescadillo homolog: i
Ribosome biogenesis protein 15: j
YTM1 isoform 1: k
25S rRNA (cytosine(2870)-C(5))-methyltransferase: l
Ribosome biogenesis protein NSA2: m
Nuclear GTP-binding protein NUG1: n
Ribosome biogenesis protein RLP7: o
Ribosome biogenesis protein RLP24: p
Nucleolar protein 16: q
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase: r
Eukaryotic translation initiation factor 6: s
UPF0642 protein YBL028C: t

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
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
y

t
z

ATP-dependent RNA helicase DBP10

60S ribosomal subunit assembly/export protein LOC1

Nucleolar complex protein 2

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

Nucleolar complex-associated protein 3

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

60S ribosomal protein L19-A

Large ribosomal subunit protein eL20A

60S ribosomal protein L22-A

60S ribosomal protein L23-A

Ribosome assembly factor MRT4

60S ribosomal protein L25

60S ribosomal protein L26-A

60S ribosomal protein L27-A

Large ribosomal subunit protein uL1A

Nucleolar GTP-binding protein 1

60S ribosomal protein L30

60S ribosomal protein L31-A

60S ribosomal protein L32

60S ribosomal protein L33-A

60S ribosomal protein L34-A

60S ribosomal protein L35-A

60S ribosomal protein L36-A

60S ribosomal protein L37-A

60S ribosomal protein L38

60S ribosome subunit biogenesis protein NIP7

Ribosome biogenesis protein ERB1

Pescadillo homolog

Ribosome biogenesis protein 15

YTM1 isoform 1

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

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Ribosome biogenesis protein RLP7

Ribosome biogenesis protein RLP24

Nucleolar protein 16

27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

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