SMTL ID : 7bt6.1

Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1)

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-mer

Ligands

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

GTP.1: 18 residues within 4Å: Chain Z: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, P.196, T.201, D.220, Q.259, N.288, K.289, S.321, C.322, Q.323 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain Z Hydrogen bonds: Z:Y.175, Z:N.177, Z:V.178, Z:G.179, Z:G.179, Z:K.180, Z:S.181, Z:S.181, Z:S.182, Z:D.220, Z:P.222, Z:N.288, Z:C.322, Z:Q.323, Z:Q.323, Z:Q.323, Z:Q.323 Salt bridges: Z:K.180, Z:K.180, Z:D.291 GTP.4: 21 residues within 4Å: Chain 9: N.260, K.261, D.263, L.264, 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, T.350, C.367 Ligands: MG.5 Chain i: U.2318 21 PLIP interactions: 21 interactions with chain 9 Hydrogen bonds: 9:N.260, 9:K.261, 9:K.261, 9:H.287, 9:A.288, 9:N.325, 9:T.326, 9:G.327, 9:K.328, 9:S.329, 9:S.329, 9:S.330, 9:A.344, 9:A.344, 9:T.350, 9:T.350, 9:T.350, 9:T.350 Salt bridges: 9:D.263, 9:K.328, 9:K.328

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain Z: Q.195, Y.197, A.198, T.200 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:Y.197, Z:T.200 MG.5: 4 residues within 4Å: Chain 9: N.325, P.347, E.349 Ligands: GTP.4 1 PLIP interactions: 1 interactions with chain 9 Metal complexes: 9:P.347

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.6: 4 residues within 4Å: Chain a: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.39, a:C.42, a:C.57, a:C.60 ZN.7: 2 residues within 4Å: Chain B: R.369 Chain c: R.33 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 L2-A: A
60S ribosomal protein L3: B
60S ribosomal protein L4-A: C
60S ribosomal protein L5: D
60S ribosomal protein L6-A: E
60S ribosomal protein L7-A: F
60S ribosomal protein L8-A: G
60S ribosomal protein L9-A: H
60S ribosomal protein L11-A: I
60S ribosomal protein L13-A: J
60S ribosomal protein L14-A: K
60S ribosomal protein L15-A: L
60S ribosomal protein L16-A: M
60S ribosomal protein L17-A: N
60S ribosomal protein L18-A: O
60S ribosomal protein L19-A: P
60S ribosomal protein L20-A: Q
60S ribosomal protein L21-A: R
60S ribosomal protein L22-A: S
60S ribosomal protein L23-A: T
Ribosome assembly factor MRT4: U
60S ribosomal protein L25: V
60S ribosomal protein L26-A: W
60S ribosomal protein L27-A: X
60S ribosomal protein L28: Y
Nucleolar GTP-binding protein 1: Z
60S ribosomal protein L30: 0
60S ribosomal protein L31-A: 1
60S ribosomal protein L32: 2
60S ribosomal protein L33-A: 3
60S ribosomal protein L34-A: 4
60S ribosomal protein L35-A: 5
60S ribosomal protein L36-A: 6
60S ribosomal protein L37-A: 7
60S ribosomal protein L38: 8
Nucleolar GTP-binding protein 2: 9
60S ribosomal protein L43-A: a
Ribosome biogenesis protein NSA2: b
Ribosome biogenesis protein RLP24: c
Ribosome biogenesis protein RPF2: d
Regulator of ribosome biosynthesis: e
Ribosome assembly protein 4: f
Eukaryotic translation initiation factor 6: g
UPF0642 protein YBL028C: h

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
J

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

T
V

U
W

V
X

W
Y

X
Z

Y
a

Z
b

0
c

1
d

2
e

3
f

4
g

5
h

6
i

7
j

8
k

9
m

a
p

b
r

c
u

d
v

e
w

f
x

g
y

h
z

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

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

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

60S ribosomal protein L43-A

Ribosome biogenesis protein NSA2

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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