SMTL ID : 6zqg.1

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x U- U- U- U- U- U- U- U- U: Poly-U RNA(Non-covalent)

U-U-U-U-U-U-U-U-U.1: 18 residues within 4Å: Chain 8: R.478, T.493, D.494, G.495, V.496, T.627, G.628, Q.629, S.736, L.737, T.761, K.783, E.784, R.785, F.796, P.906, P.1137, T.1138 Protein-ligand interaction information (PLIP) not available

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain D: C.101, C.130, H.132, C.140 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.101, D:C.130, D:H.132, D:H.132, D:C.140

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

GTP.3: 15 residues within 4Å: Chain G: 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 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:G.81, G:K.82, G:T.83, G:T.83, G:T.84, G:H.173, G:S.208 Salt bridges: G:K.82, G:K.82, G:D.175 pi-Stacking: G:H.173, G:H.173

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

MG.4: 3 residues within 4Å: Chain G: T.83, E.119 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.83, G:E.119 MG.5: 2 residues within 4Å: Chain S: C.49, A.425 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain S: G.91, G.396, G.398 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain S: G.95 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain S: A.100, U.101, A.359, C.361 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain S: U.358 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain S: G.246 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain S: G.123 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain S: C.250, A.251 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain S: G.322, G.337, A.341 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 S: A.360 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain S: A.378, U.379 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain S: A.401, C.402 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain S: G.386, C.402 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain S: G.95, G.403 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain S: C.424, G.426 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain S: C.427 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain S: U.60, G.63 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain S: A.456, G.457 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain S: A.460, G.461 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain S: A.515 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain S: A.620, A.621 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain S: A.630, G.631 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain S: A.635, A.636, A.806, A.807 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain S: A.862, A.863 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain S: U.968 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain S: A.971, G.972 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain S: C.975 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain S: A.978 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain S: U.1015 No protein-ligand interaction detected (PLIP) MG.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain S: G.1011 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain S: G.624, A.1025 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain S: G.942 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain S: U.64, C.268 Chain V: Q.176 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, J. et al., 90 S pre-ribosome transformation into the primordial 40 S subunit. Science (2020)

Release Date

2020-09-23

Peptides

Nucleolar complex protein 14: A
Something about silencing protein 10: B
Noc4,Nucleolar complex protein 4,Noc4: C
rRNA-processing protein FCF1: D
U3 small nucleolar ribonucleoprotein protein IMP4: E
U3 small nucleolar RNA-associated protein MPP10: F
Ribosome biogenesis protein BMS1: G
RNA 3'-terminal phosphate cyclase-like protein: H
Ribosomal RNA small subunit methyltransferase NEP1: IJ
Essential nuclear protein 1: K
Dimethyladenosine transferase: L
Pre-rRNA-processing protein PNO1: M
Rps5p: N
40S ribosomal protein S16-A: O
40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18: P
40S ribosomal protein S19-A: Q
40S ribosomal protein S28-A: R
40S ribosomal protein S1-A: T
40S ribosomal protein S4-A: U
40S ribosomal protein S6-A: V
40S ribosomal protein S7-A: W
40S ribosomal protein S8-A: X
40S ribosomal protein S9-A: Y
40S ribosomal protein S11-A: Z
40S ribosomal protein S13: 0
40S ribosomal protein S14-A: 1
40S ribosomal protein S25-A: 2
40S ribosomal protein S22-A: 3
40S ribosomal protein S23-A: 4
40S ribosomal protein S24-A: 5
40S ribosomal protein S27-A: 6
U3 small nucleolar RNA-associated protein 14: 7
Probable ATP-dependent RNA helicase DHR1: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
UB

B
UC

C
US

D
UX

E
CJ

F
CK

G
CL

H
CM

I
JF

J
JG

K
JH

L
JL

M
JJ

N
DF

O
DQ

P
DS

Q
DT

R
Dc

T
DA

U
DE

V
DG

W
DH

X
DI

Y
DJ

Z
DL

0
DN

1
DO

2
DZ

3
DW

4
DX

5
DY

6
Db

7
UN

8
JD

Nucleolar complex protein 14

Something about silencing protein 10

Noc4,Nucleolar complex protein 4,Noc4

rRNA-processing protein FCF1

U3 small nucleolar ribonucleoprotein protein IMP4

U3 small nucleolar RNA-associated protein MPP10

Ribosome biogenesis protein BMS1

RNA 3'-terminal phosphate cyclase-like protein

Ribosomal RNA small subunit methyltransferase NEP1

Essential nuclear protein 1

Dimethyladenosine transferase

Pre-rRNA-processing protein PNO1

Rps5p

40S ribosomal protein S16-A

40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18

40S ribosomal protein S19-A

40S ribosomal protein S28-A

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 S25-A

40S ribosomal protein S22-A

40S ribosomal protein S23-A

40S ribosomal protein S24-A

40S ribosomal protein S27-A

U3 small nucleolar RNA-associated protein 14

Probable ATP-dependent RNA helicase DHR1

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