SMTL ID : 6lqv.1

Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain g: C.101, C.130, H.132, C.140 4 PLIP interactions: 4 interactions with chain g Metal complexes: g:C.101, g:C.130, g:H.132, g:C.140

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

GTP.2: 15 residues within 4Å: Ligands: MG.3 Chain l: P.78, G.79, T.80, G.81, K.82, T.83, T.84, E.119, T.172, H.173, D.175, S.208, V.210, Y.215 14 PLIP interactions: 14 interactions with chain l Hydrogen bonds: l:G.79, l:T.80, l:T.80, l:G.81, l:G.81, l:T.83, l:T.84, l:H.173, l:V.210 Salt bridges: l:K.82, l:K.82, l:D.175 pi-Cation interactions: l:H.173, l:H.173

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Ligands: GTP.2 Chain l: T.83, E.119 2 PLIP interactions: 2 interactions with chain l Metal complexes: l:T.83, l: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 S4-A: D
40S ribosomal protein S5: E
40S ribosomal protein S6-A: F
40S ribosomal protein S8-A: G
40S ribosomal protein S9-A: H
40S ribosomal protein S11-A: I
40S ribosomal protein S16-A: J
40S ribosomal protein S23-A: K
40S ribosomal protein S24-A: L
40S ribosomal protein S28-A: M
rRNA 2'-O-methyltransferase fibrillarin: NO
Nucleolar protein 56: P
Nucleolar protein 58: Q
Ribosomal RNA-processing protein 9: R
13 kDa ribonucleoprotein-associated protein: ST
U3 small nucleolar RNA-associated protein 4: U
U3 small nucleolar RNA-associated protein 5: V
U3 small nucleolar RNA-associated protein 8: W
U3 small nucleolar RNA-associated protein 9: X
U3 small nucleolar RNA-associated protein 10: Y
U3 small nucleolar RNA-associated protein 15: Z
NET1-associated nuclear protein 1: 0
Periodic tryptophan protein 2: 1
U3 small nucleolar RNA-associated protein 12: 2
U3 small nucleolar RNA-associated protein 13: 3
U3 small nucleolar RNA-associated protein 18: 4
U3 small nucleolar RNA-associated protein 21: 5
U3 small nucleolar RNA-associated protein 6: 6
Bud site selection protein 21: 7
U3 small nucleolar RNA-associated protein 7: 8
U3 small nucleolar RNA-associated protein 11: 9
U3 small nucleolar RNA-associated protein MPP10: a
U3 small nucleolar ribonucleoprotein protein IMP3: b
U3 small nucleolar ribonucleoprotein protein IMP4: c
Something about silencing protein 10: d
Protein SOF1: e
rRNA-processing protein FCF2: f
rRNA-processing protein FCF1: g
Ribosome biogenesis protein ENP2: h
U3 small nucleolar ribonucleoprotein protein LCP5: i
Ribosomal RNA small subunit methyltransferase NEP1: jk
Ribosome biogenesis protein BMS1: l
RNA 3'-terminal phosphate cyclase-like protein: m
RNA cytidine acetyltransferase: no
Nucleolar complex protein 14: p
Nucleolar complex protein 4: q
U3 small nucleolar RNA-associated protein 20: r
U3 small nucleolar RNA-associated protein 14: s
Essential nuclear protein 1: t
Protein BFR2: u
Unassigned helices: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
SF

E
SG

F
SH

G
SJ

H
SK

I
SM

J
SR

K
SY

L
SZ

M
Sd

N
3B

O
3C

P
3D

Q
3E

R
3F

S
3G

T
3H

U
A4

V
A5

W
A8

X
A9

Y
AE

Z
AF

0
AG

1
B1

2
B2

3
B3

4
B8

5
BE

6
B6

7
5B

8
5C

9
5D

a
5E

b
5F

c
5G

d
5H

e
5I

f
5J

g
5K

h
RA

i
RB

j
RG

k
RH

l
RJ

m
RK

n
RL

o
RM

p
RN

q
RO

r
RP

s
RQ

t
RS

u
RY

v
X1

40S ribosomal protein S4-A

40S ribosomal protein S5

40S ribosomal protein S6-A

40S ribosomal protein S8-A

40S ribosomal protein S9-A

40S ribosomal protein S11-A

40S ribosomal protein S16-A

40S ribosomal protein S23-A

40S ribosomal protein S24-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 8

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

Bud site selection protein 21

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

Ribosome biogenesis protein ENP2

U3 small nucleolar ribonucleoprotein protein LCP5

Ribosomal RNA small subunit methyltransferase NEP1

Ribosome biogenesis protein BMS1

RNA 3'-terminal phosphate cyclase-like protein

RNA cytidine acetyltransferase

Nucleolar complex protein 14

Nucleolar complex protein 4

U3 small nucleolar RNA-associated protein 20

U3 small nucleolar RNA-associated protein 14

Essential nuclear protein 1

Protein BFR2

Unassigned helices

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