SMTL ID : 8ois.1

28S human mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA

Coordinates

PDB Format

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-mer

Ligands

17 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.1: 5 residues within 4Å: Chain C: C.55, C.60, C.61, C.195, G.196 Ligand excluded by PLIP K.2: 5 residues within 4Å: Chain C: G.70, A.71, G.72, G.144 Ligands: MG.17 Ligand excluded by PLIP K.3: 2 residues within 4Å: Chain C: C.834, C.839 Ligand excluded by PLIP K.4: 4 residues within 4Å: Chain C: A.551, G.552, G.553, G.774 Ligand excluded by PLIP K.5: 3 residues within 4Å: Chain C: A.551, G.552, G.715 Ligand excluded by PLIP K.6: 6 residues within 4Å: Chain C: A.609, U.610, C.683, U.688, G.689, U.690 Ligand excluded by PLIP K.7: 4 residues within 4Å: Chain C: G.528, G.529, G.829, U.830 Ligand excluded by PLIP K.8: 5 residues within 4Å: Chain C: A.917, A.918, A.926, G.939 Ligands: MG.28 Ligand excluded by PLIP K.9: 3 residues within 4Å: Chain C: U.843, G.912, U.913 Ligand excluded by PLIP K.10: 5 residues within 4Å: Chain C: C.153, A.154, C.158, C.159 Ligands: MG.34 Ligand excluded by PLIP K.11: 5 residues within 4Å: Chain C: C.188, A.190, U.191, A.192, U.203 Ligand excluded by PLIP K.12: 4 residues within 4Å: Chain 8: H.183 Chain C: A.367, A.368, G.384 Ligand excluded by PLIP K.13: 5 residues within 4Å: Chain C: G.6, U.7, A.16, G.17, C.18 Ligand excluded by PLIP K.14: 2 residues within 4Å: Chain C: U.214, U.274 Ligand excluded by PLIP K.15: 3 residues within 4Å: Chain C: C.586, C.587, G.703 Ligand excluded by PLIP K.16: 4 residues within 4Å: Chain C: C.919, A.920, A.925, A.926 Ligand excluded by PLIP K.149: 7 residues within 4Å: Chain 6: T.82, E.479, D.480, L.481, I.482, P.483, S.484 Ligand excluded by PLIP

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

MG.17: 4 residues within 4Å: Chain C: A.71, G.72, G.144 Ligands: K.2 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: U.290, A.291, A.292, A.293 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain C: G.381 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain C: A.407 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain C: A.420 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain C: C.423, A.435, G.939 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain C: A.420, A.443, U.444, G.445 No protein-ligand interaction detected (PLIP) MG.24: 5 residues within 4Å: Chain 2: Q.273 Chain C: U.612, A.679, G.680, G.681 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain C: A.619 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain C: A.787 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain C: U.916, A.917, A.918, G.923 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain C: A.918, G.923, A.925, A.926 Ligands: K.8 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain C: G.947 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain C: G.398 No protein-ligand interaction detected (PLIP) MG.31: 2 residues within 4Å: Chain C: U.300, G.398 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain C: A.658 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain C: U.608, G.698, A.699 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain C: A.154, C.159 Ligands: K.10 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Chain C: C.168, A.169 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain C: G.231, C.233, A.234, A.235 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain C: A.671, G.673 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain C: U.27, A.180, C.181 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain C: A.84 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain C: A.99 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain C: U.111, C.499 No protein-ligand interaction detected (PLIP) MG.42: 2 residues within 4Å: Chain C: C.171, G.173 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain C: C.261, G.262 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain C: G.410, G.445 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain C: C.496, U.930 No protein-ligand interaction detected (PLIP) MG.46: 1 residues within 4Å: Chain C: U.497 No protein-ligand interaction detected (PLIP) MG.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.48: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.49: 4 residues within 4Å: Chain C: G.570, A.571, G.681, U.682 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain C: C.587 No protein-ligand interaction detected (PLIP) MG.51: 5 residues within 4Å: Chain C: C.586, C.587, U.588, C.705, A.706 No protein-ligand interaction detected (PLIP) MG.52: 4 residues within 4Å: Chain C: A.611, U.612, A.679, G.680 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain C: C.667, G.668 No protein-ligand interaction detected (PLIP) MG.54: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.55: 3 residues within 4Å: Chain C: A.740, C.741, G.742 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain C: G.754 Chain M: K.59 No protein-ligand interaction detected (PLIP) MG.57: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain C: A.209 No protein-ligand interaction detected (PLIP) MG.59: 3 residues within 4Å: Chain C: G.829, U.830, G.948 No protein-ligand interaction detected (PLIP) MG.60: 4 residues within 4Å: Chain 2: E.265 Chain C: G.570, A.571, U.572 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain C: A.350 No protein-ligand interaction detected (PLIP) MG.62: 1 residues within 4Å: Chain C: G.698 No protein-ligand interaction detected (PLIP) MG.63: 3 residues within 4Å: Chain C: G.552, G.553, A.554 No protein-ligand interaction detected (PLIP) MG.64: 4 residues within 4Å: Chain C: G.240, U.241, G.242, A.258 No protein-ligand interaction detected (PLIP) MG.65: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain C: U.930 No protein-ligand interaction detected (PLIP) MG.67: 2 residues within 4Å: Chain C: A.901, G.902 No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain C: U.369, G.371 No protein-ligand interaction detected (PLIP) MG.69: 2 residues within 4Å: Chain C: G.742, A.743 No protein-ligand interaction detected (PLIP) MG.70: 2 residues within 4Å: Chain C: G.10, C.832 No protein-ligand interaction detected (PLIP) MG.71: 3 residues within 4Å: Chain C: U.8, A.521, G.522 No protein-ligand interaction detected (PLIP) MG.72: 2 residues within 4Å: Chain C: U.9, G.11 No protein-ligand interaction detected (PLIP) MG.73: 1 residues within 4Å: Chain C: A.295 No protein-ligand interaction detected (PLIP) MG.74: 4 residues within 4Å: Chain C: G.294, A.295, U.297, C.461 No protein-ligand interaction detected (PLIP) MG.75: 1 residues within 4Å: Chain C: A.400 No protein-ligand interaction detected (PLIP) MG.76: 3 residues within 4Å: Chain C: C.683, A.684, U.688 No protein-ligand interaction detected (PLIP) MG.77: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.78: 1 residues within 4Å: Chain C: U.434 No protein-ligand interaction detected (PLIP) MG.79: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.80: 2 residues within 4Å: Chain C: G.795, U.796 No protein-ligand interaction detected (PLIP) MG.81: 2 residues within 4Å: Chain C: U.924 Chain K: N.4 No protein-ligand interaction detected (PLIP) MG.82: 1 residues within 4Å: Chain C: A.67 No protein-ligand interaction detected (PLIP) MG.83: 3 residues within 4Å: Chain C: G.531, U.533 Ligands: MG.84 No protein-ligand interaction detected (PLIP) MG.84: 5 residues within 4Å: Chain C: C.530, G.531, U.533, G.827 Ligands: MG.83 No protein-ligand interaction detected (PLIP) MG.85: 3 residues within 4Å: Chain C: C.615, G.681, U.682 No protein-ligand interaction detected (PLIP) MG.86: 1 residues within 4Å: Chain C: A.249 No protein-ligand interaction detected (PLIP) MG.87: 1 residues within 4Å: Chain C: C.606 No protein-ligand interaction detected (PLIP) MG.88: 1 residues within 4Å: Chain C: U.610 No protein-ligand interaction detected (PLIP) MG.89: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.90: 1 residues within 4Å: Chain C: A.422 No protein-ligand interaction detected (PLIP) MG.91: 2 residues within 4Å: Chain C: C.578, C.579 No protein-ligand interaction detected (PLIP) MG.92: 4 residues within 4Å: Chain C: A.611, C.683, G.686, G.687 No protein-ligand interaction detected (PLIP) MG.93: 1 residues within 4Å: Chain C: A.367 No protein-ligand interaction detected (PLIP) MG.94: 2 residues within 4Å: Chain C: A.541, G.781 No protein-ligand interaction detected (PLIP) MG.95: 3 residues within 4Å: Chain C: A.794, G.795, U.796 No protein-ligand interaction detected (PLIP) MG.96: 1 residues within 4Å: Chain C: G.775 No protein-ligand interaction detected (PLIP) MG.97: 2 residues within 4Å: Chain C: U.921, A.925 No protein-ligand interaction detected (PLIP) MG.98: 1 residues within 4Å: Chain C: A.366 No protein-ligand interaction detected (PLIP) MG.99: 2 residues within 4Å: Chain C: G.793, G.802 No protein-ligand interaction detected (PLIP) MG.100: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.101: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.102: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.103: 2 residues within 4Å: Chain C: A.845, C.846 No protein-ligand interaction detected (PLIP) MG.104: 2 residues within 4Å: Chain C: U.229, G.230 No protein-ligand interaction detected (PLIP) MG.105: 3 residues within 4Å: Chain C: C.473, A.475, A.636 No protein-ligand interaction detected (PLIP) MG.106: 1 residues within 4Å: Chain C: A.204 No protein-ligand interaction detected (PLIP) MG.107: 1 residues within 4Å: Chain C: C.247 No protein-ligand interaction detected (PLIP) MG.108: 2 residues within 4Å: Chain C: G.252, A.519 No protein-ligand interaction detected (PLIP) MG.109: 1 residues within 4Å: Chain C: C.853 No protein-ligand interaction detected (PLIP) MG.110: 2 residues within 4Å: Chain C: C.89 Chain W: M.72 No protein-ligand interaction detected (PLIP) MG.111: 1 residues within 4Å: Chain C: G.163 No protein-ligand interaction detected (PLIP) MG.112: 3 residues within 4Å: Chain C: U.74, U.141, U.142 No protein-ligand interaction detected (PLIP) MG.113: 1 residues within 4Å: Chain C: C.138 No protein-ligand interaction detected (PLIP) MG.114: 1 residues within 4Å: Chain C: A.762 No protein-ligand interaction detected (PLIP) MG.115: 1 residues within 4Å: Chain C: G.559 No protein-ligand interaction detected (PLIP) MG.116: 1 residues within 4Å: Chain C: A.653 No protein-ligand interaction detected (PLIP) MG.117: 1 residues within 4Å: Chain C: U.201 No protein-ligand interaction detected (PLIP) MG.118: 2 residues within 4Å: Chain C: U.69, C.171 No protein-ligand interaction detected (PLIP) MG.119: 3 residues within 4Å: Chain C: A.328, A.329 Chain S: K.3 No protein-ligand interaction detected (PLIP) MG.120: 2 residues within 4Å: Chain C: G.296, U.454 No protein-ligand interaction detected (PLIP) MG.121: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.122: 3 residues within 4Å: Chain C: C.423, U.424, C.441 No protein-ligand interaction detected (PLIP) MG.123: 2 residues within 4Å: Chain C: U.634, U.637 No protein-ligand interaction detected (PLIP) MG.124: 3 residues within 4Å: Chain C: U.387, U.388 Ligands: MG.125 No protein-ligand interaction detected (PLIP) MG.125: 2 residues within 4Å: Chain C: U.386 Ligands: MG.124 No protein-ligand interaction detected (PLIP) MG.126: 2 residues within 4Å: Chain C: C.391, A.392 No protein-ligand interaction detected (PLIP) MG.127: 2 residues within 4Å: Chain C: G.700, G.701 No protein-ligand interaction detected (PLIP) MG.128: 2 residues within 4Å: Chain C: A.71, G.144 No protein-ligand interaction detected (PLIP) MG.129: 2 residues within 4Å: Chain C: C.288, U.290 No protein-ligand interaction detected (PLIP) MG.130: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.131: 1 residues within 4Å: Chain C: C.506 No protein-ligand interaction detected (PLIP) MG.132: 1 residues within 4Å: Chain C: G.689 No protein-ligand interaction detected (PLIP) MG.133: 3 residues within 4Å: Chain C: C.607, A.684, G.687 No protein-ligand interaction detected (PLIP) MG.134: 1 residues within 4Å: Chain C: A.465 No protein-ligand interaction detected (PLIP) MG.135: 1 residues within 4Å: Chain C: G.17 No protein-ligand interaction detected (PLIP) MG.136: 2 residues within 4Å: Chain C: C.583, G.800 No protein-ligand interaction detected (PLIP) MG.137: 3 residues within 4Å: Chain C: C.494, G.907 Chain F: N.139 No protein-ligand interaction detected (PLIP) MG.139: 1 residues within 4Å: Chain I: G.27 No protein-ligand interaction detected (PLIP) MG.143: 2 residues within 4Å: Chain W: R.64, R.68 No protein-ligand interaction detected (PLIP) MG.145: 3 residues within 4Å: Chain Z: T.135, S.311 Ligands: ATP.144 4 PLIP interactions: 1 interactions with chain Z, 3 Ligand-Water interactions Metal complexes: Z:T.135, H2O.1, H2O.1, H2O.1 MG.147: 5 residues within 4Å: Chain 3: H.93, D.224, N.226, D.240, D.241 3 PLIP interactions: 3 interactions with chain 3 Metal complexes: 3:H.93, 3:D.240, 3:D.241 MG.148: 3 residues within 4Å: Chain 5: F.229, R.237 Chain C: G.10 No protein-ligand interaction detected (PLIP)

1 x MET: METHIONINE(Non-functional Binders)

MET.138: 1 residues within 4Å: Chain I: A.71 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.140: 5 residues within 4Å: Chain Q: C.94, C.105, C.108, C.143, Q.146 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.94, Q:C.105, Q:C.108, Q:C.143

2 x FS2: FE-S-O HYBRID CLUSTER(Non-covalent)

FS2.141: 9 residues within 4Å: Chain G: C.105, G.107, I.108 Chain R: K.64, C.65, C.68, C.100, K.102, K.103 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain G, Metal complexes: R:C.65, R:C.68, R:C.100, G:C.105 FS2.142: 7 residues within 4Å: Chain O: G.25, C.26, R.29 Chain V: C.139, C.141, C.149, P.150 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain O, Metal complexes: V:C.139, V:C.141, V:C.149, O:C.26

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.144: 20 residues within 4Å: Chain Z: P.84, F.87, Q.90, L.99, M.100, R.102, K.130, G.131, T.132, G.133, K.134, T.135, L.136, S.311, T.313, Y.348, P.388, S.389, E.392 Ligands: MG.145 18 PLIP interactions: 18 interactions with chain Z Hydrogen bonds: Z:Q.90, Z:M.100, Z:M.100, Z:R.102, Z:G.131, Z:T.132, Z:T.132, Z:G.133, Z:K.134, Z:T.135, Z:L.136, Z:S.311, Z:T.313, Z:T.313, Z:Y.348 Water bridges: Z:S.311 Salt bridges: Z:K.134, Z:K.134

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.146: 10 residues within 4Å: Chain Z: Y.173, R.177, Y.208, V.209, D.238, G.241, I.242, K.245, N.292, K.295 10 PLIP interactions: 10 interactions with chain Z Hydrogen bonds: Z:V.209, Z:V.209, Z:V.209, Z:N.292, Z:N.292 Salt bridges: Z:R.177, Z:D.238, Z:K.245, Z:K.295, Z:K.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saurer, M. et al., Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Science (2023)

Release Date

2023-06-14

Peptides

39S ribosomal protein L19, mitochondrial: A
39S ribosomal protein L55, mitochondrial: B
28S ribosomal protein S35, mitochondrial: D
28S ribosomal protein S24, mitochondrial: E
Aurora kinase A-interacting protein: F
28S ribosomal protein S6, mitochondrial: G
28S ribosomal protein S7, mitochondrial: H
28S ribosomal protein S10, mitochondrial: J
28S ribosomal protein S12, mitochondrial: L
28S ribosomal protein S14, mitochondrial: M
28S ribosomal protein S15, mitochondrial: N
28S ribosomal protein S16, mitochondrial: O
28S ribosomal protein S17, mitochondrial: P
28S ribosomal protein S18b, mitochondrial: Q
28S ribosomal protein S18c, mitochondrial: R
28S ribosomal protein S21, mitochondrial: S
28S ribosomal protein S22, mitochondrial: T
28S ribosomal protein S23, mitochondrial: U
28S ribosomal protein S25, mitochondrial: V
28S ribosomal protein S26, mitochondrial: W
28S ribosomal protein S27, mitochondrial: X
28S ribosomal protein S28, mitochondrial: Y
28S ribosomal protein S29, mitochondrial: Z
28S ribosomal protein S31, mitochondrial: 0
28S ribosomal protein S33, mitochondrial: 1
Peptide chain release factor 1, mitochondrial,mtRF1(AAQ): 2
28S ribosomal protein S2, mitochondrial: 3
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1: 4
28S ribosomal protein S5, mitochondrial: 5
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 6
28S ribosomal protein S9, mitochondrial: 7
28S ribosomal protein S11, mitochondrial: 8
28S ribosomal protein S34, mitochondrial: 9

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BX

B
Bd

D
AB

E
AC

F
AD

G
AE

H
AF

J
AH

L
AJ

M
AK

N
AL

O
AM

P
AN

Q
AO

R
AP

S
AQ

T
AR

U
AS

V
AT

W
AU

X
AV

Y
AW

Z
AX

0
AY

1
AZ

2
Aa

3
Ab

4
Ac

5
Ad

6
Ae

7
Ag

8
Ai

9
Aj

39S ribosomal protein L19, mitochondrial

39S ribosomal protein L55, mitochondrial

28S ribosomal protein S35, mitochondrial

28S ribosomal protein S24, mitochondrial

Aurora kinase A-interacting protein

28S ribosomal protein S6, mitochondrial

28S ribosomal protein S7, mitochondrial

28S ribosomal protein S10, mitochondrial

28S ribosomal protein S12, mitochondrial

28S ribosomal protein S14, mitochondrial

28S ribosomal protein S15, mitochondrial

28S ribosomal protein S16, mitochondrial

28S ribosomal protein S17, mitochondrial

28S ribosomal protein S18b, mitochondrial

28S ribosomal protein S18c, mitochondrial

28S ribosomal protein S21, mitochondrial

28S ribosomal protein S22, mitochondrial

28S ribosomal protein S23, mitochondrial

28S ribosomal protein S25, mitochondrial

28S ribosomal protein S26, mitochondrial

28S ribosomal protein S27, mitochondrial

28S ribosomal protein S28, mitochondrial

28S ribosomal protein S29, mitochondrial

28S ribosomal protein S31, mitochondrial

28S ribosomal protein S33, mitochondrial

Peptide chain release factor 1, mitochondrial,mtRF1(AAQ)

28S ribosomal protein S2, mitochondrial

Coiled-coil-helix-coiled-coil-helix domain-containing protein 1

28S ribosomal protein S5, mitochondrial

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

28S ribosomal protein S9, mitochondrial

28S ribosomal protein S11, mitochondrial

28S ribosomal protein S34, mitochondrial

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