SMTL ID : 3j16.1

Models of ribosome-bound Dom34p and Rli1p and their ribosomal binding partners

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: K.116, S.117, Q.171, E.247 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.117

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.2: 14 residues within 4Å: Chain B: Y.87, S.91, F.92, N.112, G.113, I.114, G.115, K.116, S.117, T.118, E.247, H.279, S.299 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:F.92, B:N.112, B:G.113, B:G.113, B:I.114, B:G.115, B:G.115, B:K.116, B:S.117, B:T.118, B:T.118, B:S.299 Salt bridges: B:K.116, B:K.116 pi-Stacking: B:Y.87, B:Y.87

2 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.3: 13 residues within 4Å: Chain B: C.29, P.30, V.31, C.38, I.39, I.50, C.55, I.56, G.57, C.58, G.59, I.60, C.61 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.29, B:C.55, B:C.58, B:C.61 SF4.4: 10 residues within 4Å: Chain B: C.16, K.17, P.18, C.21, R.22, C.25, C.65, P.66, F.67, A.69 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.24 Metal complexes: B:C.16, B:C.21, B:C.21, B:C.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Becker, T. et al., Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. Nature (2012)

Release Date

2012-02-22

Peptides

Dom34p: A
Rli1p: B
60S ribosomal protein L6: F
40S ribosomal protein S30E: G
60S ribosomal protein L10: H
40S ribosomal protein S6E: I
60S ribosomal protein L11: J
40S ribosomal protein S24E: K
40S ribosomal protein S24-A: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F
F

G
E

H
G

I
C

J
H

K
I

L
D

Dom34p

Rli1p

60S ribosomal protein L6

40S ribosomal protein S30E

60S ribosomal protein L10

40S ribosomal protein S6E

60S ribosomal protein L11

40S ribosomal protein S24E

40S ribosomal protein S24-A

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