SMTL ID : 7d5s.1

Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

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

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

GTP.2: 15 residues within 4Å: Ligands: MG.3 Chain n: 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 n Hydrogen bonds: n:G.79, n:T.80, n:T.80, n:G.81, n:G.81, n:T.83, n:T.84, n:H.173, n:V.210 Salt bridges: n:K.82, n:K.82, n:D.175 pi-Cation interactions: n:H.173, n:H.173

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, K., Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2). To Be Published

Release Date

2021-10-06

Peptides

40S ribosomal protein S5: D
40S ribosomal protein S9-A: E
40S ribosomal protein S12: F
40S ribosomal protein S13: G
40S ribosomal protein S14-A: H
40S ribosomal protein S16-A: I
40S ribosomal protein S18-A: J
40S ribosomal protein S23-A: K
40S ribosomal protein S28-A: L
rRNA 2'-O-methyltransferase fibrillarin: MN
Nucleolar protein 56: O
Nucleolar protein 58: P
Ribosomal RNA-processing protein 9: Q
13 kDa ribonucleoprotein-associated protein: RS
U3 small nucleolar RNA-associated protein 4: T
U3 small nucleolar RNA-associated protein 5: U
U3 small nucleolar RNA-associated protein 8: V
U3 small nucleolar RNA-associated protein 9: W
U3 small nucleolar RNA-associated protein 10: X
U3 small nucleolar RNA-associated protein 15: Y
NET1-associated nuclear protein 1: Z
Periodic tryptophan protein 2: 0
U3 small nucleolar RNA-associated protein 12: 1
U3 small nucleolar RNA-associated protein 13: 2
U3 small nucleolar RNA-associated protein 18: 3
U3 small nucleolar RNA-associated protein 21: 4
U3 small nucleolar RNA-associated protein 6: 5
Bud site selection protein 21: 6
U3 small nucleolar RNA-associated protein 7: 7
U3 small nucleolar RNA-associated protein 11: 8
U3 small nucleolar RNA-associated protein MPP10: 9
U3 small nucleolar ribonucleoprotein protein IMP3: a
U3 small nucleolar ribonucleoprotein protein IMP4: b
Something about silencing protein 10: c
Protein SOF1: d
rRNA-processing protein FCF2: e
rRNA-processing protein FCF1: f
KRR1 small subunit processome component: g
rRNA biogenesis protein RRP5: h
U3 small nucleolar RNA-associated protein 22: i
Ribosomal RNA-processing protein 7: j
Ribosomal RNA small subunit methyltransferase NEP1: kl
Ribosome biogenesis protein UTP30: m
Ribosome biogenesis protein BMS1: n
RNA 3'-terminal phosphate cyclase-like protein: o
Nucleolar complex protein 14: p
Nucleolar complex protein 4: q
U3 small nucleolar RNA-associated protein 14: r
Essential nuclear protein 1: s
Pno1: t
Regulator of rDNA transcription protein 14: u
Unassigned peptides 1: v

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
SG

E
SK

F
SN

G
SO

H
SP

I
SR

J
ST

K
SY

L
Sd

M
3B

N
3C

O
3D

P
3E

Q
3F

R
3G

S
3H

T
A4

U
A5

V
A8

W
A9

X
AE

Y
AF

Z
AG

0
B1

1
B2

2
B3

3
B8

4
BE

5
B6

6
5B

7
5C

8
5D

9
5E

a
5F

b
5G

c
5H

d
5I

e
5J

f
5K

g
RC

h
RD

i
RE

j
RF

k
RG

l
RH

m
RI

n
RJ

o
RK

p
RN

q
RO

r
RQ

s
RS

t
RT

u
RW

v
X1

40S ribosomal protein S5

40S ribosomal protein S9-A

40S ribosomal protein S12

40S ribosomal protein S13

40S ribosomal protein S14-A

40S ribosomal protein S16-A

40S ribosomal protein S18-A

40S ribosomal protein S23-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

KRR1 small subunit processome component

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 UTP30

Ribosome biogenesis protein BMS1

RNA 3'-terminal phosphate cyclase-like protein

Nucleolar complex protein 14

Nucleolar complex protein 4

U3 small nucleolar RNA-associated protein 14

Essential nuclear protein 1

Pno1

Regulator of rDNA transcription protein 14

Unassigned peptides 1

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