SMTL ID : 7wtt.1

Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 24 residues within 4Å: Chain 2: P.14, Y.18, Y.26, Q.36, G.61, C.62, G.63, T.64, G.65, L.66, S.67, D.82, I.83, S.84, M.87, G.103, D.104, M.105, I.122, S.123, A.124, W.127, L.128 Chain A: G.1639 12 PLIP interactions: 12 interactions with chain 2 Hydrogen bonds: 2:Y.26, 2:Q.36, 2:C.62, 2:G.63, 2:T.64, 2:G.65, 2:L.66, 2:S.67, 2:I.83, 2:S.84, 2:D.104, 2:M.105

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain 5: C.121, S.123, C.126, C.141, C.144 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.121, 5:C.126, 5:C.141, 5:C.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, J. et al., The nucleoplasmic phase of pre-40S formation prior to nuclear export. Nucleic Acids Res. (2022)

Release Date

2022-10-19

Peptides

40S ribosomal protein S17: B
40S ribosomal protein S27: C
40S ribosomal protein S3a: D
40S ribosomal protein S28: E
40S ribosomal protein S4, X isoform: F
40S ribosomal protein S30: G
40S ribosomal protein S5: H
40S ribosomal protein S7: I
40S ribosomal protein S6: J
40S ribosomal protein S25: K
40S ribosomal protein S24: L
RNA-binding protein PNO1: M
40S ribosomal protein S23: N
Bystin: O
40S ribosomal protein S15a: P
Pre-rRNA-processing protein TSR1 homolog: Q
Protein LTV1 homolog: R
40S ribosomal protein S19: S
40S ribosomal protein S18: T
40S ribosomal protein S16: U
40S ribosomal protein S15: V
40S ribosomal protein S14: W
40S ribosomal protein S13: X
40S ribosomal protein S11: Y
40S ribosomal protein S9: Z
40S ribosomal protein S8: 0
Multifunctional methyltransferase subunit TRM112-like protein: 1
Probable 18S rRNA (guanine-N(7))-methyltransferase: 2
RRP12-like protein: 3
40S ribosomal protein S12: 4
Ubiquitin-40S ribosomal protein S27a: 5
Casein kinase I isoform alpha: 6
Ribosome biogenesis protein SLX9 homolog: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
R

C
b

D
B

E
c

F
E

G
e

H
F

I
H

J
G

K
Z

L
Y

M
x

N
X

O
w

P
W

Q
u

R
t

S
T

T
S

U
Q

V
P

W
O

X
N

Y
L

Z
J

0
I

1
r

2
q

3
K

4
M

5
f

6
a

7
z

40S ribosomal protein S17

40S ribosomal protein S27

40S ribosomal protein S3a

40S ribosomal protein S28

40S ribosomal protein S4, X isoform

40S ribosomal protein S30

40S ribosomal protein S5

40S ribosomal protein S7

40S ribosomal protein S6

40S ribosomal protein S25

40S ribosomal protein S24

RNA-binding protein PNO1

40S ribosomal protein S23

Bystin

40S ribosomal protein S15a

Pre-rRNA-processing protein TSR1 homolog

Protein LTV1 homolog

40S ribosomal protein S19

40S ribosomal protein S18

40S ribosomal protein S16

40S ribosomal protein S15

40S ribosomal protein S14

40S ribosomal protein S13

40S ribosomal protein S11

40S ribosomal protein S9

40S ribosomal protein S8

Multifunctional methyltransferase subunit TRM112-like protein

Probable 18S rRNA (guanine-N(7))-methyltransferase

RRP12-like protein

40S ribosomal protein S12

Ubiquitin-40S ribosomal protein S27a

Casein kinase I isoform alpha

Ribosome biogenesis protein SLX9 homolog

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