SMTL ID : 6em1.1

State C (Nsa1-TAP Flag-Ytm1) - 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-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain K: C.6, C.9, C.32, R.33, C.36 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.9, K:C.32, K:C.36 ZN.2: 4 residues within 4Å: Chain Y: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.19, Y:C.22, Y:C.34, Y: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

Ribosome production factor 1: A
60S ribosomal protein L7-A: B
Protein MAK16: C
Ribosomal RNA-processing protein 1: D
Ribosome biogenesis protein NSA1: E
Ribosome biogenesis protein BRX1: F
Nucleolar GTP-binding protein 1: G
rRNA-processing protein EBP2: H
Ribosome biogenesis protein NSA2: I
Nuclear GTP-binding protein NUG1: J
Ribosome biogenesis protein RLP24: K
Nucleolar protein 16: L
Ribosome assembly factor MRT4: M
Eukaryotic translation initiation factor 6: N
UPF0642 protein YBL028C: O
60S ribosomal protein L3: P
60S ribosomal protein L4-A: Q
60S ribosomal protein L32: R
60S ribosomal protein L6-A: S
60S ribosomal protein L33-A: T
60S ribosomal protein L8-A: U
60S ribosomal protein L35-A: V
60S ribosomal protein L9-A: W
60S ribosomal protein L36-B: X
60S ribosomal protein L37-A: Y
60S ribosomal protein L13-A: Z
60S ribosomal protein L14-A: 0
60S ribosomal protein L15-A: 1
60S ribosomal protein L16-A: 2
60S ribosomal protein L17-A: 3
60S ribosomal protein L18-A: 4
60S ribosomal protein L20-A: 5
60S ribosomal protein L23-A: 6
60S ribosomal protein L26-A: 7
Proteasome-interacting protein CIC1: b
Ribosome biogenesis protein ERB1: c
ATP-dependent RNA helicase HAS1: d
Ribosome biogenesis protein 15: e
Pescadillo homolog: f
Ribosome biogenesis protein RLP7: g

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
x

B
F

C
3

D
4

E
5

F
A

G
b

H
J

I
r

J
s

K
u

L
v

M
W

N
y

O
z

P
B

Q
C

R
e

S
E

T
f

U
G

V
h

W
H

X
i

Y
j

Z
L

0
M

1
N

2
O

3
P

4
Q

5
S

6
V

7
Y

b
K

c
m

d
D

e
o

f
n

g
t

Ribosome production factor 1

60S ribosomal protein L7-A

Protein MAK16

Ribosomal RNA-processing protein 1

Ribosome biogenesis protein NSA1

Ribosome biogenesis protein BRX1

Nucleolar GTP-binding protein 1

rRNA-processing protein EBP2

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Ribosome biogenesis protein RLP24

Nucleolar protein 16

Ribosome assembly factor MRT4

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L32

60S ribosomal protein L6-A

60S ribosomal protein L33-A

60S ribosomal protein L8-A

60S ribosomal protein L35-A

60S ribosomal protein L9-A

60S ribosomal protein L36-B

60S ribosomal protein L37-A

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 L23-A

60S ribosomal protein L26-A

Proteasome-interacting protein CIC1

Ribosome biogenesis protein ERB1

ATP-dependent RNA helicase HAS1

Ribosome biogenesis protein 15

Pescadillo homolog

Ribosome biogenesis protein RLP7

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