SMTL ID : 8d8j.1

Yeast mitochondrial small subunit assembly intermediate (State 1)

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-mer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 6 residues within 4Å: Chain A: C.373, P.374, C.379, P.380, C.400, C.513 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.373, A:C.379, A:C.400, A:C.513

29 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain O: U.165, G.166 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain O: A.174 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain O: A.117, C.118, A.119, A.376 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain O: C.118, A.119, U.120, U.178, G.179 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain O: A.180, G.181, U.182, A.358 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain O: A.223, A.264 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain O: G.319, U.320, G.334, U.335, U.336 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain O: U.359 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain O: C.384, G.385, U.387, G.388 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain O: C.384, G.385, U.400 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain O: A.419, C.420, A.421 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain O: C.423, G.425 No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain O: C.440, U.443, G.444, U.455 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain O: G.726 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain O: U.555, G.556 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain O: C.680 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain O: U.681 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain O: U.736, A.738 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain O: U.744, A.745, A.746, A.747 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain O: G.754 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain O: A.84, U.85, G.705 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain O: G.375, A.376, A.377, C.378, G.379 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain O: A.683, U.685, A.686, A.687 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain O: G.179, A.180, G.181, A.358 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harper, N.J. et al., Principles of mitoribosomal small subunit assembly in eukaryotes. Nature (2023)

Release Date

2022-12-21

Peptides

Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial: A
37S ribosomal protein MRP13, mitochondrial: B
Mitochondrial group I intron splicing factor CCM1: C
37S ribosomal protein S28, mitochondrial: D
37S ribosomal protein S16, mitochondrial: E
37S ribosomal protein S17, mitochondrial: F
37S ribosomal protein RSM18, mitochondrial: G
37S ribosomal protein PET123, mitochondrial: H
Protein FYV4, mitochondrial: I
37S ribosomal protein NAM9, mitochondrial: J
37S ribosomal protein S5, mitochondrial: K
37S ribosomal protein MRP17, mitochondrial: L
37S ribosomal protein S35, mitochondrial: M
37S ribosomal protein S8, mitochondrial: N
uS12m: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
5

C
d

D
O

E
P

F
Q

G
R

H
V

I
2

J
D

K
E

L
F

M
6

N
H

P
L

Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial

37S ribosomal protein MRP13, mitochondrial

Mitochondrial group I intron splicing factor CCM1

37S ribosomal protein S28, mitochondrial

37S ribosomal protein S16, mitochondrial

37S ribosomal protein S17, mitochondrial

37S ribosomal protein RSM18, mitochondrial

37S ribosomal protein PET123, mitochondrial

Protein FYV4, mitochondrial

37S ribosomal protein NAM9, mitochondrial

37S ribosomal protein S5, mitochondrial

37S ribosomal protein MRP17, mitochondrial

37S ribosomal protein S35, mitochondrial

37S ribosomal protein S8, mitochondrial

uS12m

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