SMTL ID : 7wtl.1

Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Dis-D

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-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain N: V.54, T.55, C.56, I.62, L.63 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:I.62

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

GTP.2: 15 residues within 4Å: Chain Q: P.78, G.79, T.80, G.81, K.82, T.83, T.84, E.119, T.172, H.173, D.175, L.176, V.210, Y.215 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain Q Hydrogen bonds: Q:T.80, Q:G.81, Q:K.82, Q:T.83, Q:T.83, Q:H.173 Salt bridges: Q:K.82, Q:K.82, Q:D.175 pi-Stacking: Q:H.173, Q:H.173

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain Q: T.83 Ligands: GTP.2 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, J. et al., In vitro structural maturation of an early stage pre-40S particle coupled with U3 snoRNA release and central pseudoknot formation. Nucleic Acids Res. (2022)

Release Date

2022-10-19

Peptides

40S ribosomal protein S1-A: B
40S ribosomal protein S4-A: C
40S ribosomal protein S6-A: D
40S ribosomal protein S7-A: E
40S ribosomal protein S8-A: F
40S ribosomal protein S9-A: G
40S ribosomal protein S11-A: H
40S ribosomal protein S13: I
40S ribosomal protein S14-A: J
40S ribosomal protein S22-A: K
40S ribosomal protein S23-A: L
40S ribosomal protein S24-A: M
40S ribosomal protein S27-A: N
Pre-rRNA-processing protein PNO1: O
U3 small nucleolar RNA-associated protein MPP10: P
Ribosome biogenesis protein BMS1: Q
Something about silencing protein 10: R
Dimethyladenosine transferase: S

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
SB

C
SE

D
SG

E
SH

F
SI

G
SJ

H
SL

I
SN

J
SO

K
SW

L
SX

M
SY

N
Sb

O
CA

P
CK

Q
CL

R
UC

S
JL

40S ribosomal protein S1-A

40S ribosomal protein S4-A

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 S22-A

40S ribosomal protein S23-A

40S ribosomal protein S24-A

40S ribosomal protein S27-A

Pre-rRNA-processing protein PNO1

U3 small nucleolar RNA-associated protein MPP10

Ribosome biogenesis protein BMS1

Something about silencing protein 10

Dimethyladenosine transferase

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