SMTL ID : 7btb.1

Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

GTP.1: 23 residues within 4Å: Chain 0: Y.175, N.177, V.178, G.179, K.180, S.181, S.182, D.193, V.194, P.196, T.200, T.201, D.220, T.221, P.222, Q.259, K.289, D.291, I.292, S.321, C.322, Q.323 Ligands: MG.2 25 PLIP interactions: 25 interactions with chain 0 Hydrogen bonds: 0:Y.175, 0:N.177, 0:V.178, 0:G.179, 0:K.180, 0:S.181, 0:S.181, 0:S.181, 0:S.182, 0:S.182, 0:V.194, 0:V.194, 0:T.200, 0:T.201, 0:T.201, 0:T.201, 0:P.222, 0:Q.259, 0:Q.259, 0:Q.259, 0:K.289, 0:C.322, 0:Q.323 Salt bridges: 0:K.180, 0:D.291 GTP.4: 21 residues within 4Å: Ligands: MG.5 Chain a: N.260, K.261, D.263, H.287, A.288, N.325, T.326, G.327, K.328, S.329, S.330, Q.342, V.343, A.344, P.345, P.347, E.349, T.350, C.367 Chain n: U.2318 19 PLIP interactions: 19 interactions with chain a Hydrogen bonds: a:N.260, a:K.261, a:K.261, a:A.288, a:N.325, a:T.326, a:G.327, a:K.328, a:S.329, a:S.329, a:S.330, a:P.347, a:E.349, a:T.350, a:T.350, a:T.350 Salt bridges: a:D.263, a:K.328, a:K.328

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain 0: V.194, Q.195, T.200 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain 0 Metal complexes: 0:V.194, 0:Q.195 MG.5: 6 residues within 4Å: Ligands: GTP.4 Chain a: N.325, A.344, I.346, P.347, E.349 2 PLIP interactions: 2 interactions with chain a Metal complexes: a:A.344, a:I.346

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain 8: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.19, 8:C.22, 8:C.34, 8:C.37 ZN.6: 5 residues within 4Å: Chain d: C.39, C.42, C.57, C.59, C.60 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.39, d:C.42, d:C.57, d:C.59 ZN.7: 3 residues within 4Å: Chain D: R.369 Chain h: R.33, W.51 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilson, D.M. et al., Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel. Nat Commun (2020)

Release Date

2020-10-28

Peptides

60S ribosomal protein L13-A: A
60S ribosomal protein L28: B
60S ribosomal protein L2-A: C
60S ribosomal protein L3: D
60S ribosomal protein L4-A: E
60S ribosomal protein L5: F
60S ribosomal protein L6-A: G
60S ribosomal protein L7-A: H
60S ribosomal protein L8-A: I
60S ribosomal protein L9-A: J
60S ribosomal protein L11-A: K
Proteasome-interacting protein CIC1: L
60S ribosomal protein L14-A: M
60S ribosomal protein L15-A: N
60S ribosomal protein L16-A: O
60S ribosomal protein L17-A: P
60S ribosomal protein L18-A: Q
60S ribosomal protein L19-A: R
60S ribosomal protein L20-A: S
60S ribosomal protein L21-A: T
60S ribosomal protein L22-A: U
60S ribosomal protein L23-A: V
Ribosome assembly factor MRT4: W
60S ribosomal protein L25: X
60S ribosomal protein L26-A: Y
60S ribosomal protein L27-A: Z
Nucleolar GTP-binding protein 1: 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 L35-A: 6
60S ribosomal protein L36-A: 7
60S ribosomal protein L37-A: 8
60S ribosomal protein L38: 9
Nucleolar GTP-binding protein 2: a
Pescadillo homolog: b
Ribosome biogenesis protein 15: c
60S ribosomal protein L43-A: d
Ribosome biogenesis protein NOP53: e
Ribosome biogenesis protein NSA2: f
Ribosome biogenesis protein RLP7: g
Ribosome biogenesis protein RLP24: h
Ribosome biogenesis protein RPF2: i
Regulator of ribosome biosynthesis: j
Ribosome assembly protein 4: k
Eukaryotic translation initiation factor 6: l
UPF0642 protein YBL028C: m

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
a

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
J

L
K

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

0
b

1
c

2
d

3
e

4
f

5
g

6
h

7
i

8
j

9
k

a
m

b
n

c
o

d
p

e
q

f
r

g
t

h
u

i
v

j
w

k
x

l
y

m
z

60S ribosomal protein L13-A

60S ribosomal protein L28

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

60S ribosomal protein L11-A

Proteasome-interacting protein CIC1

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

Nucleolar GTP-binding protein 1

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 L35-A

60S ribosomal protein L36-A

60S ribosomal protein L37-A

60S ribosomal protein L38

Nucleolar GTP-binding protein 2

Pescadillo homolog

Ribosome biogenesis protein 15

60S ribosomal protein L43-A

Ribosome biogenesis protein NOP53

Ribosome biogenesis protein NSA2

Ribosome biogenesis protein RLP7

Ribosome biogenesis protein RLP24

Ribosome biogenesis protein RPF2

Regulator of ribosome biosynthesis

Ribosome assembly protein 4

Eukaryotic translation initiation factor 6

UPF0642 protein YBL028C

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