SMTL ID : 6ri5.1

Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles

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-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain 5: C.44, C.47, C.81, C.84 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:C.44, 5:C.47, 5:C.84 ZN.2: 4 residues within 4Å: Chain 7: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.19, 7:C.22, 7:C.34, 7:C.37 ZN.3: 5 residues within 4Å: Chain a: C.12, C.17, T.21, C.74, C.77 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.12, a:C.17, a:C.74, a:C.77 ZN.4: 4 residues within 4Å: Chain b: C.39, C.42, C.57, C.60 3 PLIP interactions: 3 interactions with chain b Metal complexes: b:C.39, b:C.57, b:C.60 ZN.5: 5 residues within 4Å: Chain e: C.58, C.61, Q.142, C.143, C.146 No protein-ligand interaction detected (PLIP) ZN.6: 6 residues within 4Å: Chain e: C.19, C.22, G.23, P.25, C.35, C.38 2 PLIP interactions: 2 interactions with chain e Metal complexes: e:C.19, e:C.35 ZN.7: 4 residues within 4Å: Chain j: C.96, C.99, C.110, C.115 3 PLIP interactions: 3 interactions with chain j Metal complexes: j:C.96, j:C.99, j:C.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kargas, V. et al., Mechanism of completion of peptidyltransferase centre assembly in eukaryotes. Elife (2019)

Release Date

2019-06-26

Peptides

60S ribosomal protein L2-A: B
60S ribosomal protein L3: C
60S ribosomal protein L4-A: D
60S ribosomal protein L11-A: E
60S ribosomal protein L9-A: F
60S ribosomal protein L6-A: G
60S ribosomal protein L8-A: H
60S ribosomal protein L16-B: I
60S ribosomal protein L13-A: J
60S ribosomal protein L23-A: K
60S ribosomal protein L14-A: L
60S ribosomal protein L28: M
60S ribosomal protein L15-A: N
60S ribosomal protein L5: O
60S ribosomal protein L18-A: P
60S ribosomal protein L19-A: Q
60S ribosomal protein L20-A: R
60S ribosomal protein L21-A: S
60S ribosomal protein L17-A: T
60S ribosomal protein L22-A: U
60S ribosomal protein L25: V
60S ribosomal protein L26-A: W
60S ribosomal protein L27-A: X
60S ribosomal protein L35-A: Y
60S ribosomal protein L29: Z
60S ribosomal protein L7-A: 0
60S ribosomal protein L30: 1
60S ribosomal protein L31-A: 2
60S ribosomal protein L32: 3
60S ribosomal protein L33-A: 4
60S ribosomal protein L34-A: 5
60S ribosomal protein L36-A: 6
60S ribosomal protein L37-A: 7
60S ribosomal protein L38: 8
60S ribosomal protein L39: 9
60S ribosomal protein L42-A: a
60S ribosomal protein L43-A: b
Eukaryotic translation initiation factor 6: c
Cytoplasmic 60S subunit biogenesis factor REH1: d
60S ribosomal export protein NMD3: e
60S ribosomal protein L24-A: f
Large subunit GTPase 1: g
uL1: h
60S ribosomal protein L10: i
Ubiquitin-60S ribosomal protein L40: j

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
J

J
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

S
T

T
U

U
V

V
W

W
X

X
Y

Y
Z

Z
a

0
b

1
c

2
d

3
e

4
f

5
g

6
h

7
i

8
j

9
k

a
l

b
m

c
n

d
z

e
w

f
v

g
o

h
p

i
q

j
t

60S ribosomal protein L2-A

60S ribosomal protein L3

60S ribosomal protein L4-A

60S ribosomal protein L11-A

60S ribosomal protein L9-A

60S ribosomal protein L6-A

60S ribosomal protein L8-A

60S ribosomal protein L16-B

60S ribosomal protein L13-A

60S ribosomal protein L23-A

60S ribosomal protein L14-A

60S ribosomal protein L28

60S ribosomal protein L15-A

60S ribosomal protein L5

60S ribosomal protein L18-A

60S ribosomal protein L19-A

60S ribosomal protein L20-A

60S ribosomal protein L21-A

60S ribosomal protein L17-A

60S ribosomal protein L22-A

60S ribosomal protein L25

60S ribosomal protein L26-A

60S ribosomal protein L27-A

60S ribosomal protein L35-A

60S ribosomal protein L29

60S ribosomal protein L7-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 L39

60S ribosomal protein L42-A

60S ribosomal protein L43-A

Eukaryotic translation initiation factor 6

Cytoplasmic 60S subunit biogenesis factor REH1

60S ribosomal export protein NMD3

60S ribosomal protein L24-A

Large subunit GTPase 1

uL1

60S ribosomal protein L10

Ubiquitin-60S ribosomal protein L40

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