SMTL ID : 9n78.1

SSU processome maturation and disassembly, State L

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 2 residues within 4Å: Chain B: G.362, G.377 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain B: U.88 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: C.79, A.80 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain B: U.82 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: A.428 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: G.868 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: G.1101 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain B: U.1603, U.1604 Chain m: D.95, E.144 1 PLIP interactions: 1 interactions with chain m Metal complexes: m:E.144 MG.10: 4 residues within 4Å: Chain B: G.363, G.377, A.378, U.379 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: A.635, A.636 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: G.516 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: A.475 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: G.1014 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain B: A.104 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain B: U.120 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: 1 residues within 4Å: Chain J: T.161 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain B: G.1035 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain B: G.938 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain B: A.341 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain B: C.31 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain B: A.1587, G.1588 Chain m: D.95 No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain B: A.401 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain B: C.49, A.425 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain B: C.424, G.426 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain B: A.93, G.95, G.403 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain B: G.386, C.402 Chain E: R.3 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain B: C.427 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain B: U.358 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain B: A.515 No protein-ligand interaction detected (PLIP) MG.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain B: A.100, U.101, A.360, C.361 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain B: A.862, A.863 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain B: 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 B: A.630, G.631 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Ligands: GTP.48 Chain i: T.83, E.119 2 PLIP interactions: 2 interactions with chain i Metal complexes: i:T.83, i:E.119

2 x ZN: ZINC ION(Non-covalent)

ZN.47: 4 residues within 4Å: Chain 5: C.37, G.39, C.40, C.59 3 PLIP interactions: 3 interactions with chain 5 Metal complexes: 5:C.37, 5:C.40, 5:C.59 ZN.50: 4 residues within 4Å: Chain l: C.101, C.130, H.132, C.140 4 PLIP interactions: 4 interactions with chain l Metal complexes: l:C.101, l:C.130, l:H.132, l:C.140

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

GTP.48: 15 residues within 4Å: Ligands: MG.49 Chain i: G.79, 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 15 PLIP interactions: 15 interactions with chain i Hydrogen bonds: i:G.79, i:T.80, i:G.81, i:K.82, i:T.83, i:T.83, i:T.84, i:H.173, i:S.208, i:Y.215 Salt bridges: i:K.82, i:K.82, i:D.175 pi-Stacking: i:H.173, i: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: 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 S16-A: K
40S ribosomal protein S11-A: L
40S ribosomal protein S22-A: M
40S ribosomal protein S24-A: N
40S ribosomal protein S28-A: O
NET1-associated nuclear protein 1: P
U3 small nucleolar RNA-associated protein 8: Q
U3 small nucleolar RNA-associated protein 15: R
U3 small nucleolar RNA-associated protein 9: S
U3 small nucleolar RNA-associated protein 5: T
U3 small nucleolar RNA-associated protein 10: U
U3 small nucleolar RNA-associated protein 4: V
U3 small nucleolar RNA-associated protein 18: W
U3 small nucleolar RNA-associated protein MPP10: X
Something about silencing protein 10: Y
Bud site selection protein 21: Z
40S ribosomal protein S13: 0
40S ribosomal protein S14-A: 1
Dimethyladenosine transferase: 2
Small ribosomal subunit protein eS1A: 3
40S ribosomal protein S19-A: 4
40S ribosomal protein S27-A: 5
Probable ATP-dependent RNA helicase DHR1: 6
Exosome complex exonuclease RRP6: 7
40S ribosomal protein S12: 8
Ubiquitin-40S ribosomal protein S31: 9
Nucleolar protein 56: a
Nucleolar protein 58: b
rRNA 2'-O-methyltransferase fibrillarin: cd
13 kDa ribonucleoprotein-associated protein: ef
Ribosomal RNA-processing protein 9: g
RNA 3'-terminal phosphate cyclase-like protein: h
Ribosome biogenesis protein BMS1: i
Ribosomal RNA small subunit methyltransferase NEP1: jk
rRNA-processing protein FCF1: l
U3 small nucleolar ribonucleoprotein protein IMP4: m
U3 small nucleolar RNA-associated protein 20: n
rRNA-processing protein FCF2: o
40S ribosomal protein S23-A: p
U3 small nucleolar RNA-associated protein 14: q
Nucleolar complex protein 14: r
Nucleolar complex protein 4: s
Regulator of rDNA transcription protein 14: t
Pre-rRNA-processing protein PNO1: u
U3 small nucleolar RNA-associated protein 11: v
Essential nuclear protein 1: w

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
L3

E
L4

F
L5

G
L6

H
L7

I
L8

J
L9

K
LC

L
LD

M
LE

N
LF

O
LG

P
LH

Q
LI

R
LJ

S
LK

T
LL

U
LM

V
LN

W
LS

X
NA

Y
NB

Z
ND

0
NF

1
NG

2
NL

3
NM

4
NP

5
NQ

6
NS

7
NV

8
OH

9
OU

a
SA

b
SB

c
SC

d
SD

e
SE

f
SF

g
SG

h
SH

i
SI

j
SJ

k
SK

l
SL

m
SM

n
SP

o
SQ

p
SR

q
SS

r
ST

s
SU

t
SV

u
SW

v
SY

w
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

NET1-associated nuclear protein 1

U3 small nucleolar RNA-associated protein 8

U3 small nucleolar RNA-associated protein 15

U3 small nucleolar RNA-associated protein 9

U3 small nucleolar RNA-associated protein 5

U3 small nucleolar RNA-associated protein 10

U3 small nucleolar RNA-associated protein 4

U3 small nucleolar RNA-associated protein 18

U3 small nucleolar RNA-associated protein MPP10

Something about silencing protein 10

Bud site selection protein 21

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

Exosome complex exonuclease RRP6

40S ribosomal protein S12

Ubiquitin-40S ribosomal protein S31

Nucleolar protein 56

Nucleolar protein 58

rRNA 2'-O-methyltransferase fibrillarin

13 kDa ribonucleoprotein-associated protein

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

rRNA-processing protein FCF2

40S ribosomal protein S23-A

U3 small nucleolar RNA-associated protein 14

Nucleolar complex protein 14

Nucleolar complex protein 4

Regulator of rDNA transcription protein 14

Pre-rRNA-processing protein PNO1

U3 small nucleolar RNA-associated protein 11

Essential nuclear protein 1

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