SMTL ID : 6ylg.1

Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement)

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-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain N: C.51, C.54, H.67, H.73 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.51, N:C.54, N:H.67 ZN.4: 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 ZN.7: 5 residues within 4Å: Chain k: C.39, C.42, C.57, C.59, C.60 4 PLIP interactions: 4 interactions with chain k Metal complexes: k:C.39, k:C.42, k:C.57, k:C.59 ZN.8: 5 residues within 4Å: Chain p: C.6, C.9, C.32, R.33, C.36 3 PLIP interactions: 3 interactions with chain p Metal complexes: p:C.6, p:C.32, p:C.36

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)(Non-covalent)

GTP.2: 18 residues within 4Å: Chain 6: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, V.194, T.201, D.220, T.221, P.222, N.288, S.321, C.322, Q.323 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain 6 Hydrogen bonds: 6:N.177, 6:V.178, 6:G.179, 6:G.179, 6:K.180, 6:S.181, 6:S.182, 6:T.201, 6:T.201, 6:T.201, 6:P.222, 6:N.288, 6:C.322 Salt bridges: 6:K.180, 6:K.180 GTP.5: 24 residues within 4Å: Chain A: A.2317, U.2318 Ligands: MG.6 Chain h: N.260, K.261, D.263, L.264, H.287, A.288, P.324, N.325, T.326, G.327, K.328, S.329, S.330, Q.342, V.343, A.344, P.345, P.347, T.350, D.366, C.367 20 PLIP interactions: 20 interactions with chain h Hydrogen bonds: h:N.260, h:K.261, h:K.261, h:A.288, h:N.325, h:T.326, h:T.326, h:G.327, h:K.328, h:S.329, h:S.329, h:S.330, h:S.330, h:A.344, h:T.350, h:T.350, h:C.367 Salt bridges: h:D.263, h:K.328, h:K.328

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain 6: N.177, Q.195, Y.197, A.198, T.200 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain 6 Metal complexes: 6:Y.197, 6:T.200 MG.6: 3 residues within 4Å: Ligands: GTP.5 Chain h: N.325, P.347 1 PLIP interactions: 1 interactions with chain h Metal complexes: h:P.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kater, L. et al., Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. Mol.Cell (2020)

Release Date

2020-07-29

Peptides

Probable metalloprotease ARX1: D
rRNA-processing protein CGR1: E
60S ribosomal protein L2-A: F
60S ribosomal protein L3: G
60S ribosomal protein L4-A: H
60S ribosomal protein L5: I
60S ribosomal protein L6-A: J
60S ribosomal protein L7-A: K
60S ribosomal protein L8-A: L
60S ribosomal protein L9-A: M
Bud site selection protein 20: N
60S ribosomal protein L11-A: O
Pre-rRNA-processing protein IPI1: P
60S ribosomal protein L13-A: Q
60S ribosomal protein L14-A: R
60S ribosomal protein L15-A: S
60S ribosomal protein L16-A: T
60S ribosomal protein L17-A: U
60S ribosomal protein L18-A: V
60S ribosomal protein L19-A: W
60S ribosomal protein L20-A: X
60S ribosomal protein L21-A: 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
60S ribosomal protein L28: 5
Nucleolar GTP-binding protein 1: 6
Ribosome biogenesis protein ALB1: 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 ribosomal protein L39: g
Nucleolar GTP-binding protein 2: h
60S ribosomal protein L30: i
60S ribosomal protein L1-A: j
60S ribosomal protein L43-A: k
60S ribosomal protein L12-A: l
Ribosome biogenesis protein NSA2: m
Nuclear GTP-binding protein NUG1: n
Protein SDA1: o
Ribosome biogenesis protein RLP24: p
Ribosome assembly protein 4: q
Eukaryotic translation initiation factor 6: r
UPF0642 protein YBL028C: s

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
4

E
5

F
A

G
B

H
C

I
D

J
E

K
F

L
G

M
H

N
I

O
J

P
K

Q
L

R
M

S
N

T
O

U
P

V
Q

W
R

X
S

Y
T

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
x

r
y

s
z

Probable metalloprotease ARX1

rRNA-processing protein CGR1

60S ribosomal protein L2-A

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L5

60S ribosomal protein L6-A

60S ribosomal protein L7-A

60S ribosomal protein L8-A

60S ribosomal protein L9-A

Bud site selection protein 20

60S ribosomal protein L11-A

Pre-rRNA-processing protein IPI1

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 L19-A

60S ribosomal protein L20-A

60S ribosomal protein L21-A

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

60S ribosomal protein L28

Nucleolar GTP-binding protein 1

Ribosome biogenesis protein ALB1

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 ribosomal protein L39

Nucleolar GTP-binding protein 2

60S ribosomal protein L30

60S ribosomal protein L1-A

60S ribosomal protein L43-A

60S ribosomal protein L12-A

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

Protein SDA1

Ribosome biogenesis protein RLP24

Ribosome assembly protein 4

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

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