SMTL ID : 6elz.1

State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

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-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kater, L. et al., Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell (2017)

Release Date

2017-12-27

Peptides

60S ribosomal protein L13-A: D
60S ribosomal protein L15-A: E
60S ribosomal protein L18-A: F
60S ribosomal protein L19-A: G
60S ribosomal protein L20-A: H
60S ribosomal protein L21-A: I
60S ribosomal protein L22-A: J
60S ribosomal protein L27-A: K
60S ribosomal protein L30: L
60S ribosomal protein L31-A: M
60S ribosomal protein L32: N
60S ribosomal protein L33-A: O
60S ribosomal protein L34-A: P
60S ribosomal protein L36-A: Q
60S ribosomal protein L37-A: R
60S ribosomal protein L38: S
60S ribosomal protein L16-A: T
60S ribosomal protein L23-A: U
60S ribosomal protein L28: V
60S ribosomal protein L17-A: W
60S ribosomal protein L25: X
60S ribosomal protein L26-A: Y
60S ribosomal protein L35-A: Z
60S ribosomal protein L7-A: 0
60S ribosomal protein L3: 1
60S ribosomal protein L4-A: 2
60S ribosomal protein L9-A: 3
Ribosome biogenesis protein BRX1: 4
Proteasome-interacting protein CIC1: 5
Ribosome biogenesis protein ERB1: 6
ATP-dependent RNA helicase HAS1: 7
Ribosome assembly factor MRT4: 8
60S ribosome subunit biogenesis protein NIP7: 9
Nucleolar GTP-binding protein 1: a
Ribosome biogenesis protein 15: b
Pescadillo homolog: c
Ribosome biogenesis protein NSA2: d
Nuclear GTP-binding protein NUG1: e
Ribosome biogenesis protein RLP7: f
Eukaryotic translation initiation factor 6: g
UPF0642 protein YBL028C: h
Ribosome biogenesis protein YTM1: i
25S rRNA (cytosine(2870)-C(5))-methyltransferase: j
Ribosome biogenesis protein RLP24: k
Nucleolar protein 16: l
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase: m
Nucleolar complex-associated protein 3: n
rRNA-processing protein EBP2: o
60S ribosomal protein L6-A: p
60S ribosomal protein L8-A: q
60S ribosomal protein L14-A: r

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
L

E
N

F
Q

G
R

H
S

I
T

J
U

K
Z

L
c

M
d

N
e

O
f

P
g

Q
i

R
j

S
k

T
O

U
V

V
a

W
P

X
X

Y
Y

Z
h

0
F

1
B

2
C

3
H

4
A

5
K

6
m

7
D

8
W

9
l

a
b

b
o

c
n

d
r

e
s

f
t

g
y

h
z

i
p

j
q

k
u

l
v

m
w

n
I

o
J

p
E

q
G

r
M

60S ribosomal protein L13-A

60S ribosomal protein L15-A

60S ribosomal protein L18-A

60S ribosomal protein L19-A

60S ribosomal protein L20-A

60S ribosomal protein L21-A

60S ribosomal protein L22-A

60S ribosomal protein L27-A

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 L36-A

60S ribosomal protein L37-A

60S ribosomal protein L38

60S ribosomal protein L16-A

60S ribosomal protein L23-A

60S ribosomal protein L28

60S ribosomal protein L17-A

60S ribosomal protein L25

60S ribosomal protein L26-A

60S ribosomal protein L35-A

60S ribosomal protein L7-A

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L9-A

Ribosome biogenesis protein BRX1

Proteasome-interacting protein CIC1

Ribosome biogenesis protein ERB1

ATP-dependent RNA helicase HAS1

Ribosome assembly factor MRT4

60S ribosome subunit biogenesis protein NIP7

Nucleolar GTP-binding protein 1

Ribosome biogenesis protein 15

Pescadillo homolog

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Ribosome biogenesis protein RLP7

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

Ribosome biogenesis protein YTM1

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

Ribosome biogenesis protein RLP24

Nucleolar protein 16

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

Nucleolar complex-associated protein 3

rRNA-processing protein EBP2

60S ribosomal protein L6-A

60S ribosomal protein L8-A

60S ribosomal protein L14-A

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