SMTL ID : 9n7a.1

SSU processome maturation and disassembly, State N

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x U- U- U- U- U: U3snoRNA segment(Non-covalent)

U-U-U-U-U.1: 17 residues within 4Å: Chain W: P.450, R.451, R.452, R.478, T.493, G.495, V.496, R.499, T.627, G.628, Q.629, Y.735, S.736, T.761, K.783, R.785, P.906 Protein-ligand interaction information (PLIP) not available

47 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: G.362, G.377 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: U.88 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: A.80 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: A.428 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: G.1101 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain 4: R.94, E.144 Chain A: U.1603, U.1604 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain A: G.377, A.378, U.379 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: A.635, A.636, A.806 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain A: C.36 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: A.475, A.544 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: G.985, G.1014 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain A: U.795 No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain A: U.1617 No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain A: G.1035 No protein-ligand interaction detected (PLIP) MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain A: G.322, A.341 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain A: C.31 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain 4: D.95 Chain A: A.1587 No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: A.387, A.400, A.401 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: C.49, A.425 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain A: C.424, G.426 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain A: A.93, G.95, G.403 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Chain A: G.386, C.402 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain A: C.427 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain A: U.358 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain A: A.515 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain A: G.337 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain A: G.876 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain A: A.100, U.101, C.361 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain A: A.862, A.863 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain A: G.63 No protein-ligand interaction detected (PLIP) MG.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain A: A.630, G.631 No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain A: C.975 No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain 0: T.83, E.119 Ligands: GTP.49 2 PLIP interactions: 2 interactions with chain 0 Metal complexes: 0:T.83, 0:E.119

2 x ZN: ZINC ION(Non-covalent)

ZN.48: 4 residues within 4Å: Chain V: C.37, G.39, C.40, C.59 No protein-ligand interaction detected (PLIP) ZN.51: 4 residues within 4Å: Chain 3: C.101, C.130, H.132, C.140 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:C.101, 3:C.130, 3:H.132, 3:C.140

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

GTP.49: 17 residues within 4Å: Chain 0: P.78, G.79, T.80, G.81, K.82, T.83, T.84, E.119, T.172, H.173, D.175, L.176, S.208, G.209, V.210, Y.215 Ligands: MG.50 15 PLIP interactions: 15 interactions with chain 0 Hydrogen bonds: 0:G.79, 0:G.81, 0:K.82, 0:T.83, 0:T.83, 0:T.83, 0:T.84, 0:H.173, 0:S.208, 0:Y.215 Salt bridges: 0:K.82, 0:K.82, 0:D.175 pi-Stacking: 0:H.173, 0:H.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buzovetsky, O. et al., Mechanism of helicase-mediated SSU processome maturation and disassembly. To Be Published

Release Date

2025-11-05

Peptides

40S ribosomal protein S18-A: C
40S ribosomal protein S4-A: D
40S ribosomal protein S5: E
40S ribosomal protein S6-A: F
40S ribosomal protein S7-A: G
40S ribosomal protein S8-A: H
40S ribosomal protein S9-A: I
40S ribosomal protein S16-A: J
40S ribosomal protein S11-A: K
40S ribosomal protein S22-A: L
40S ribosomal protein S24-A: M
40S ribosomal protein S28-A: N
U3 small nucleolar RNA-associated protein MPP10: O
Something about silencing protein 10: P
40S ribosomal protein S13: Q
40S ribosomal protein S14-A: R
Dimethyladenosine transferase: S
Small ribosomal subunit protein eS1A: T
40S ribosomal protein S19-A: U
40S ribosomal protein S27-A: V
Probable ATP-dependent RNA helicase DHR1: W
40S ribosomal protein S25-A: X
Ribosomal RNA-processing protein 9: Y
RNA 3'-terminal phosphate cyclase-like protein: Z
Ribosome biogenesis protein BMS1: 0
Ribosomal RNA small subunit methyltransferase NEP1: 12
rRNA-processing protein FCF1: 3
U3 small nucleolar ribonucleoprotein protein IMP4: 4
U3 small nucleolar RNA-associated protein 20: 5
40S ribosomal protein S23-A: 6
U3 small nucleolar RNA-associated protein 14: 7
Nucleolar complex protein 14: 8
Nucleolar complex protein 4: 9
Pre-rRNA-processing protein PNO1: a
Essential nuclear protein 1: b

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
L3

D
L4

E
L5

F
L6

G
L7

H
L8

I
L9

J
LC

K
LD

L
LE

M
LF

N
LG

O
NA

P
NB

Q
NF

R
NG

S
NL

T
NM

U
NP

V
NQ

W
NS

X
NW

Y
SG

Z
SH

0
SI

1
SJ

2
SK

3
SL

4
SM

5
SP

6
SR

7
SS

8
ST

9
SU

a
SW

b
SZ

40S ribosomal protein S18-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 S16-A

40S ribosomal protein S11-A

40S ribosomal protein S22-A

40S ribosomal protein S24-A

40S ribosomal protein S28-A

U3 small nucleolar RNA-associated protein MPP10

Something about silencing protein 10

40S ribosomal protein S13

40S ribosomal protein S14-A

Dimethyladenosine transferase

Small ribosomal subunit protein eS1A

40S ribosomal protein S19-A

40S ribosomal protein S27-A

Probable ATP-dependent RNA helicase DHR1

40S ribosomal protein S25-A

Ribosomal RNA-processing protein 9

RNA 3'-terminal phosphate cyclase-like protein

Ribosome biogenesis protein BMS1

Ribosomal RNA small subunit methyltransferase NEP1

rRNA-processing protein FCF1

U3 small nucleolar ribonucleoprotein protein IMP4

U3 small nucleolar RNA-associated protein 20

40S ribosomal protein S23-A

U3 small nucleolar RNA-associated protein 14

Nucleolar complex protein 14

Nucleolar complex protein 4

Pre-rRNA-processing protein PNO1

Essential nuclear protein 1

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