SMTL ID : 6m62.1

Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain O: C.51, C.54, H.67, H.73 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.51, O:C.54, O:H.67, O:H.73 ZN.4: 4 residues within 4Å: Chain f: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.19, f:C.22, f:C.34, f:C.37 ZN.7: 4 residues within 4Å: Chain l: C.39, C.42, C.57, C.59 4 PLIP interactions: 4 interactions with chain l Metal complexes: l:C.39, l:C.42, l:C.57, l:C.59 ZN.8: 4 residues within 4Å: Chain A: G.3333 Chain q: R.33, K.35, W.51 No protein-ligand interaction detected (PLIP)

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

GTP.2: 27 residues within 4Å: Chain 7: Y.175, P.176, N.177, V.178, G.179, K.180, S.181, S.182, D.193, V.194, Y.197, A.198, F.199, T.200, T.201, D.220, T.221, P.222, Q.259, N.288, K.289, D.291, S.320, S.321, C.322, Q.323 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain 7 Hydrogen bonds: 7:N.177, 7:V.178, 7:G.179, 7:K.180, 7:S.181, 7:S.182, 7:S.182, 7:V.194, 7:T.200, 7:T.201, 7:T.221, 7:N.288, 7:K.289, 7:K.289, 7:K.289, 7:C.322, 7:Q.323 Salt bridges: 7:D.291 GTP.5: 20 residues within 4Å: Ligands: MG.6 Chain i: 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, E.349, T.350 17 PLIP interactions: 17 interactions with chain i Hydrogen bonds: i:N.260, i:K.261, i:A.288, i:T.326, i:G.327, i:K.328, i:S.329, i:S.330, i:S.330, i:A.344, i:A.344, i:E.349, i:T.350, i:T.350 Salt bridges: i:D.263, i:K.328, i:K.328

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain 7: V.194, Q.195, T.200 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Ligands: GTP.5 Chain i: P.324, N.325, T.326, K.328, P.347 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Micic, J. et al., Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly. Nat Commun (2020)

Release Date

2020-08-26

Peptides

Probable metalloprotease ARX1: D
rRNA-processing protein CGR1: E
60S ribosomal protein L2-A: G
60S ribosomal protein L3: H
60S ribosomal protein L4-A: I
60S ribosomal protein L5: J
60S ribosomal protein L6-A: K
60S ribosomal protein L7-A: L
60S ribosomal protein L8-A: M
60S ribosomal protein L9-A: N
Bud site selection protein 20: O
60S ribosomal protein L11-A: P
Proteasome-interacting protein CIC1: Q
60S ribosomal protein L13-A: R
60S ribosomal protein L14-A: S
60S ribosomal protein L15-A: T
60S ribosomal protein L16-A: U
60S ribosomal protein L17-A: V
60S ribosomal protein L18-A: W
60S ribosomal protein L19-A: X
60S ribosomal protein L20-A: Y
60S ribosomal protein L21-A: Z
60S ribosomal protein L22-A: 0
60S ribosomal protein L23-A: 1
Ribosome assembly factor MRT4: 2
60S ribosomal protein L25: 3
60S ribosomal protein L26-A: 4
60S ribosomal protein L27-A: 5
60S ribosomal protein L28: 6
Nucleolar GTP-binding protein 1: 7
60S ribosomal protein L30: 8
60S ribosomal protein L31-A: 9
60S ribosomal protein L32: a
60S ribosomal protein L33-A: b
60S ribosomal protein L34-A: c
60S ribosomal protein L35-A: d
60S ribosomal protein L36-A: e
60S ribosomal protein L37-A: f
60S ribosomal protein L38: g
60S ribosomal protein L39: h
Nucleolar GTP-binding protein 2: i
Pescadillo homolog: j
Ribosome biogenesis protein 15: k
60S ribosomal protein L43-A: l
Ribosome biogenesis protein NOP53: m
Ribosome biogenesis protein NSA2: n
Nuclear GTP-binding protein NUG1: o
Ribosome biogenesis protein RLP7: p
Ribosome biogenesis protein RLP24: q
Ribosome biogenesis protein RPF2: r
Regulator of ribosome biosynthesis: s
Ribosome assembly protein 4: t
Eukaryotic translation initiation factor 6: u
UPF0642 protein YBL028C: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
4

E
5

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

O
I

P
J

Q
K

R
L

S
M

T
N

U
O

V
P

W
Q

X
R

Y
S

Z
T

0
U

1
V

2
W

3
X

4
Y

5
Z

6
a

7
b

8
c

9
d

a
e

b
f

c
g

d
h

e
i

f
j

g
k

h
l

i
m

j
n

k
o

l
p

m
q

n
r

o
s

p
t

q
u

r
v

s
w

t
x

u
y

v
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

Proteasome-interacting protein CIC1

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

60S ribosomal protein L39

Nucleolar GTP-binding protein 2

Pescadillo homolog

Ribosome biogenesis protein 15

60S ribosomal protein L43-A

Ribosome biogenesis protein NOP53

Ribosome biogenesis protein NSA2

Nuclear GTP-binding protein NUG1

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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