SMTL ID : 6n8k.1

Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit

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-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain F: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, V.194, P.196, Y.197, A.198, T.200, T.201, D.220, T.221, P.222, N.288, K.289, D.291, S.321, C.322 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:Y.175, F:N.177, F:N.177, F:V.178, F:G.179, F:K.180, F:S.181, F:S.181, F:S.182, F:S.182, F:P.196, F:T.200, F:T.201, F:T.201, F:T.201, F:N.288, F:C.322 Salt bridges: F:K.180, F:K.180, F:D.291

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain F: Q.195, Y.197, T.200 Ligands: GTP.1 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:Q.195, F:Y.197, F:T.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Nat Commun (2019)

Release Date

2019-03-13

Peptides

Ribosomal Protein uL1: A
60S ribosomal export protein NMD3: B
60S ribosomal protein L2-A: C
60S ribosomal protein L28: D
60S ribosomal protein L3: E
Nucleolar GTP-binding protein 1: F
60S ribosomal protein L4-A: G
60S ribosomal protein L30: H
60S ribosomal protein L31-A: I
60S ribosomal protein L6-A: J
60S ribosomal protein L32: K
60S ribosomal protein L7-A: L
60S ribosomal protein L33-A: M
60S ribosomal protein L8-A: N
60S ribosomal protein L34-A: O
Bud site selection protein 20: P
60S ribosomal protein L9-A: Q
60S ribosomal protein L35-A: R
60S ribosomal protein L36-A: S
60S ribosomal protein L37-A: T
60S ribosomal protein L38: U
60S ribosomal protein L13-A: V
60S ribosomal protein L39: W
60S ribosomal protein L14-A: X
60S ribosomal protein L43-A: Y
60S ribosomal protein L15-A: Z
Ribosome biogenesis protein RLP24: 0
60S ribosomal protein L16-A: 1
60S ribosomal protein L17-A: 2
60S ribosomal protein L18-A: 3
60S ribosomal protein L19-A: 4
60S ribosomal protein L20-A: 5
60S ribosomal protein L21-A: 6
60S ribosomal protein L22-A: 7
60S ribosomal protein L23-A: 8
Ribosome assembly factor MRT4: 9
60S ribosomal protein L25: a
60S ribosomal protein L26-A: b
Eukaryotic translation initiation factor 6: c
60S ribosomal protein L27-A: d
UPF0642 protein YBL028C: e
60S ribosomal protein L5: f
60S ribosomal protein L11-A: g
60S ribosomal protein L42-A: h
60S ribosomal protein L29: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
s

B
v

C
A

D
a

E
B

F
b

G
C

H
c

I
d

J
E

K
e

L
F

M
f

N
G

O
g

P
I

Q
H

R
h

S
i

T
j

U
k

V
L

W
l

X
M

Y
p

Z
N

0
u

1
O

2
P

3
Q

4
R

5
S

6
T

7
U

8
V

9
W

a
X

b
Y

c
y

d
Z

e
z

f
D

g
J

h
q

i
o

Ribosomal Protein uL1

60S ribosomal export protein NMD3

60S ribosomal protein L2-A

60S ribosomal protein L28

60S ribosomal protein L3

Nucleolar GTP-binding protein 1

60S ribosomal protein L4-A

60S ribosomal protein L30

60S ribosomal protein L31-A

60S ribosomal protein L6-A

60S ribosomal protein L32

60S ribosomal protein L7-A

60S ribosomal protein L33-A

60S ribosomal protein L8-A

60S ribosomal protein L34-A

Bud site selection protein 20

60S ribosomal protein L9-A

60S ribosomal protein L35-A

60S ribosomal protein L36-A

60S ribosomal protein L37-A

60S ribosomal protein L38

60S ribosomal protein L13-A

60S ribosomal protein L39

60S ribosomal protein L14-A

60S ribosomal protein L43-A

60S ribosomal protein L15-A

Ribosome biogenesis protein RLP24

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

Eukaryotic translation initiation factor 6

60S ribosomal protein L27-A

UPF0642 protein YBL028C

60S ribosomal protein L5

60S ribosomal protein L11-A

60S ribosomal protein L42-A

60S ribosomal protein L29

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