SMTL ID : 6lqt.1

Cryo-EM structure of 90S small subunit preribosomes in transition states (State E)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain R: C.37, G.39, C.40, N.42, S.58, C.59 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:C.37, R:C.40, R:C.40 ZN.2: 5 residues within 4Å: Chain k: C.101, C.130, H.132, C.140, R.144 3 PLIP interactions: 3 interactions with chain k Metal complexes: k:C.101, k:H.132, k:C.140

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

GTP.3: 14 residues within 4Å: Ligands: MG.4 Chain p: G.79, T.80, G.81, K.82, T.83, T.84, E.119, H.173, D.175, S.208, G.209, V.210, Y.215 12 PLIP interactions: 12 interactions with chain p Hydrogen bonds: p:G.79, p:T.80, p:G.81, p:K.82, p:T.83, p:T.84, p:H.173, p:V.210 Salt bridges: p:K.82, p:D.175 pi-Stacking: p:H.173 pi-Cation interactions: p:H.173

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Ligands: GTP.3 Chain p: T.83, E.119 2 PLIP interactions: 2 interactions with chain p Metal complexes: p:T.83, p:E.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, Y. et al., Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states. Science (2020)

Release Date

2020-09-16

Peptides

40S ribosomal protein S1-A: D
40S ribosomal protein S4-A: E
40S ribosomal protein S5: F
40S ribosomal protein S6-A: G
40S ribosomal protein S7-A: H
40S ribosomal protein S8-A: I
40S ribosomal protein S9-A: J
40S ribosomal protein S11-A: K
40S ribosomal protein S13: L
40S ribosomal protein S14-A: M
40S ribosomal protein S16-A: N
40S ribosomal protein S22-B: O
40S ribosomal protein S23-A: P
40S ribosomal protein S24-A: Q
40S ribosomal protein S27-A: R
40S ribosomal protein S28-A: S
rRNA 2'-O-methyltransferase fibrillarin: TU
Nucleolar protein 56: V
Nucleolar protein 58: W
Ribosomal RNA-processing protein 9: X
13 kDa ribonucleoprotein-associated protein: YZ
U3 small nucleolar RNA-associated protein 4: 0
U3 small nucleolar RNA-associated protein 5: 1
U3 small nucleolar RNA-associated protein 9: 2
U3 small nucleolar RNA-associated protein 10: 3
U3 small nucleolar RNA-associated protein 15: 4
NET1-associated nuclear protein 1: 5
Periodic tryptophan protein 2: 6
U3 small nucleolar RNA-associated protein 12: 7
U3 small nucleolar RNA-associated protein 13: 8
U3 small nucleolar RNA-associated protein 18: 9
U3 small nucleolar RNA-associated protein 21: a
U3 small nucleolar RNA-associated protein 6: b
U3 small nucleolar RNA-associated protein 7: c
U3 small nucleolar RNA-associated protein 11: d
U3 small nucleolar RNA-associated protein MPP10: e
U3 small nucleolar ribonucleoprotein protein IMP3: f
U3 small nucleolar ribonucleoprotein protein IMP4: g
Something about silencing protein 10: h
Protein SOF1: i
rRNA-processing protein FCF2: j
rRNA-processing protein FCF1: k
rRNA biogenesis protein RRP5: l
U3 small nucleolar RNA-associated protein 22: m
Ribosomal RNA-processing protein 7: n
Ribosomal RNA small subunit methyltransferase NEP1: o
Ribosome biogenesis protein BMS1: p
RNA 3'-terminal phosphate cyclase-like protein: q
Nucleolar complex protein 14: r
U3 small nucleolar RNA-associated protein 20: s
U3 small nucleolar RNA-associated protein 14: t
Pno1: u
Unassigned helices: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
SC

E
SF

F
SG

G
SH

H
SI

I
SJ

J
SK

K
SM

L
SO

M
SP

N
SR

O
SX

P
SY

Q
SZ

R
Sc

S
Sd

T
3B

U
3C

V
3D

W
3E

X
3F

Y
3G

Z
3H

0
A4

1
A5

2
A9

3
AE

4
AF

5
AG

6
B1

7
B2

8
B3

9
B8

a
BE

b
B6

c
5C

d
5D

e
5E

f
5F

g
5G

h
5H

i
5I

j
5J

k
5K

l
RD

m
RE

n
RF

o
RH

p
RJ

q
RK

r
RN

s
RP

t
RQ

u
RT

v
X1

40S ribosomal protein S1-A

40S ribosomal protein S4-A

40S ribosomal protein S5

40S ribosomal protein S6-A

40S ribosomal protein S7-A

40S ribosomal protein S8-A

40S ribosomal protein S9-A

40S ribosomal protein S11-A

40S ribosomal protein S13

40S ribosomal protein S14-A

40S ribosomal protein S16-A

40S ribosomal protein S22-B

40S ribosomal protein S23-A

40S ribosomal protein S24-A

40S ribosomal protein S27-A

40S ribosomal protein S28-A

rRNA 2'-O-methyltransferase fibrillarin

Nucleolar protein 56

Nucleolar protein 58

Ribosomal RNA-processing protein 9

13 kDa ribonucleoprotein-associated protein

U3 small nucleolar RNA-associated protein 4

U3 small nucleolar RNA-associated protein 5

U3 small nucleolar RNA-associated protein 9

U3 small nucleolar RNA-associated protein 10

U3 small nucleolar RNA-associated protein 15

NET1-associated nuclear protein 1

Periodic tryptophan protein 2

U3 small nucleolar RNA-associated protein 12

U3 small nucleolar RNA-associated protein 13

U3 small nucleolar RNA-associated protein 18

U3 small nucleolar RNA-associated protein 21

U3 small nucleolar RNA-associated protein 6

U3 small nucleolar RNA-associated protein 7

U3 small nucleolar RNA-associated protein 11

U3 small nucleolar RNA-associated protein MPP10

U3 small nucleolar ribonucleoprotein protein IMP3

U3 small nucleolar ribonucleoprotein protein IMP4

Something about silencing protein 10

Protein SOF1

rRNA-processing protein FCF2

rRNA-processing protein FCF1

rRNA biogenesis protein RRP5

U3 small nucleolar RNA-associated protein 22

Ribosomal RNA-processing protein 7

Ribosomal RNA small subunit methyltransferase NEP1

Ribosome biogenesis protein BMS1

RNA 3'-terminal phosphate cyclase-like protein

Nucleolar complex protein 14

U3 small nucleolar RNA-associated protein 20

U3 small nucleolar RNA-associated protein 14

Pno1

Unassigned helices

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