SMTL ID : 7nac.1

State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model

Coordinates

PDB Format

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

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain 1: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.19, 1:C.22, 1:C.34, 1:C.37 ZN.2: 4 residues within 4Å: Chain k: C.44, C.47, C.81, C.84 4 PLIP interactions: 4 interactions with chain k Metal complexes: k:C.44, k:C.47, k:C.81, k:C.84

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.3: 18 residues within 4Å: Chain A: G.2922 Chain s: S.29, D.52, C.54, A.55, A.56, P.57, G.58, S.59, W.60, D.78, I.79, V.80, D.94, I.95, D.119, A.121, L.138 12 PLIP interactions: 12 interactions with chain s Hydrophobic interactions: s:D.119 Hydrogen bonds: s:S.29, s:D.52, s:G.58, s:S.59, s:W.60, s:I.79, s:D.94, s:D.94, s:I.95, s:D.119, s:D.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cruz, V.E. et al., Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-09

Peptides

60S ribosomal subunit assembly/export protein LOC1: C
Ribosome biogenesis protein BRX1: D
60S ribosomal protein L3: E
60S ribosomal protein L4-A: F
60S ribosomal protein L6-A: G
60S ribosomal protein L7-A: H
60S ribosomal protein L9-A: I
rRNA-processing protein EBP2: J
60S ribosomal protein L13-A: K
60S ribosomal protein L14-A: L
60S ribosomal protein L15-A: M
60S ribosomal protein L16-A: N
60S ribosomal protein L17-A: O
60S ribosomal protein L18-A: P
60S ribosomal protein L20-A: Q
60S ribosomal protein L21-A: R
Ribosome assembly factor MRT4: S
60S ribosomal protein L25: T
60S ribosomal protein L26-A: U
Nucleolar GTP-binding protein 1: V
60S ribosomal protein L31-A: W
60S ribosomal protein L32: X
60S ribosomal protein L33-A: Y
60S ribosomal protein L35-A: Z
60S ribosomal protein L36-A: 0
60S ribosomal protein L37-A: 1
60S ribosome subunit biogenesis protein NIP7: 2
Ribosome biogenesis protein ERB1: 3
25S rRNA (cytosine(2870)-C(5))-methyltransferase: 4
Ribosome biogenesis protein NSA2: 5
Nuclear GTP-binding protein NUG1: 6
Ribosome biogenesis protein RLP24: 7
Nucleolar protein 16: 8
Eukaryotic translation initiation factor 6: 9
UPF0642 protein YBL028C: a
NOC2 isoform 1: b
Nucleolar complex-associated protein 3: c
Proteasome-interacting protein CIC1: d
60S ribosomal protein L23-A: e
60S ribosomal protein L19-A: f
60S ribosomal protein L8-A: g
60S ribosomal protein L27-A: h
60S ribosomal protein L22-A: i
60S ribosomal protein L30: j
60S ribosomal protein L34-A: k
60S ribosomal protein L38: l
Pescadillo homolog: m
YTM1 isoform 1: n
Ribosome biogenesis protein RLP7: o
ATP-dependent RNA helicase HAS1: q
Ribosome biogenesis protein 15: r
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase: s
Ribosomal protein: t
RRP17 isoform 1: u
ATP-dependent rRNA helicase SPB4: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
7

D
A

E
B

F
C

G
E

H
F

I
H

J
J

K
L

L
M

M
N

N
O

O
P

P
Q

Q
S

R
T

S
W

T
X

U
Y

V
b

W
d

X
e

Y
f

Z
h

0
i

1
j

2
l

3
m

4
q

5
r

6
s

7
u

8
v

9
y

a
z

b
8

c
I

d
K

e
V

f
R

g
G

h
Z

i
U

j
c

k
g

l
k

m
n

n
p

o
t

q
D

r
o

s
w

t
a

u
5

v
x

60S ribosomal subunit assembly/export protein LOC1

Ribosome biogenesis protein BRX1

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L6-A

60S ribosomal protein L7-A

60S ribosomal protein L9-A

rRNA-processing protein EBP2

60S ribosomal protein L13-A

60S ribosomal protein L14-A

60S ribosomal protein L15-A

60S ribosomal protein L16-A

60S ribosomal protein L17-A

60S ribosomal protein L18-A

60S ribosomal protein L20-A

60S ribosomal protein L21-A

Ribosome assembly factor MRT4

60S ribosomal protein L25

60S ribosomal protein L26-A

Nucleolar GTP-binding protein 1

60S ribosomal protein L31-A

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

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

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Ribosome biogenesis protein RLP24

Nucleolar protein 16

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

NOC2 isoform 1

Nucleolar complex-associated protein 3

Proteasome-interacting protein CIC1

60S ribosomal protein L23-A

60S ribosomal protein L19-A

60S ribosomal protein L8-A

60S ribosomal protein L27-A

60S ribosomal protein L22-A

60S ribosomal protein L30

60S ribosomal protein L34-A

60S ribosomal protein L38

Pescadillo homolog

YTM1 isoform 1

Ribosome biogenesis protein RLP7

ATP-dependent RNA helicase HAS1

Ribosome biogenesis protein 15

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

Ribosomal protein

RRP17 isoform 1

ATP-dependent rRNA helicase SPB4

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