SMTL ID : 7d5t.1

Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1)

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-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain R: C.37, G.39, C.40, N.42, C.56, S.58, C.59 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.37, R:C.40, R:S.58, R:C.59 ZN.2: 4 residues within 4Å: Chain h: C.101, C.130, H.132, C.140 3 PLIP interactions: 3 interactions with chain h Metal complexes: h:C.130, h:H.132, h:C.140

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

GTP.3: 14 residues within 4Å: Ligands: MG.4 Chain l: P.78, G.79, T.80, G.81, K.82, T.83, T.84, E.119, H.173, S.208, G.209, V.210, Y.215 12 PLIP interactions: 12 interactions with chain l Hydrogen bonds: l:G.79, l:T.83, l:T.83, l:T.83, l:T.84, l:H.173, l:V.210 Salt bridges: l:K.82, l:K.82 pi-Stacking: l:H.173, l:H.173 pi-Cation interactions: l:H.173

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 19 residues within 4Å: Chain r: E.415, T.416, G.417, S.418, G.419, K.420, T.421, T.422, S.457, M.458, E.460, R.461, F.747, T.766, S.767, L.768, T.769, I.770, P.771 13 PLIP interactions: 13 interactions with chain r Hydrogen bonds: r:E.415, r:G.417, r:S.418, r:S.418, r:G.419, r:K.420, r:T.421, r:T.421, r:T.422, r:E.460, r:R.461 Salt bridges: r:K.420 pi-Stacking: r:F.747

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, K., Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1). To Be Published

Release Date

2021-10-06

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 5: 0
U3 small nucleolar RNA-associated protein 10: 1
NET1-associated nuclear protein 1: 2
Periodic tryptophan protein 2: 3
U3 small nucleolar RNA-associated protein 12: 4
U3 small nucleolar RNA-associated protein 13: 5
U3 small nucleolar RNA-associated protein 18: 6
U3 small nucleolar RNA-associated protein 21: 7
U3 small nucleolar RNA-associated protein 6: 8
U3 small nucleolar RNA-associated protein 7: 9
U3 small nucleolar RNA-associated protein 11: a
U3 small nucleolar RNA-associated protein MPP10: b
U3 small nucleolar ribonucleoprotein protein IMP3: c
U3 small nucleolar ribonucleoprotein protein IMP4: d
Something about silencing protein 10: e
Protein SOF1: f
rRNA-processing protein FCF2: g
rRNA-processing protein FCF1: h
rRNA biogenesis protein RRP5: i
U3 small nucleolar RNA-associated protein 22: j
Ribosomal RNA-processing protein 7: k
Ribosome biogenesis protein BMS1: l
RNA 3'-terminal phosphate cyclase-like protein: m
Nucleolar complex protein 14: n
U3 small nucleolar RNA-associated protein 20: o
U3 small nucleolar RNA-associated protein 14: p
Pno1: q
Probable ATP-dependent RNA helicase DHR1: r
Unassigned peptides 1: s

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
A5

1
AE

2
AG

3
B1

4
B2

5
B3

6
B8

7
BE

8
B6

9
5C

a
5D

b
5E

c
5F

d
5G

e
5H

f
5I

g
5J

h
5K

i
RD

j
RE

k
RF

l
RJ

m
RK

n
RN

o
RP

p
RQ

q
RT

r
RZ

s
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 5

U3 small nucleolar RNA-associated protein 10

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

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

Probable ATP-dependent RNA helicase DHR1

Unassigned peptides 1

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